- galaxy-user - lists.galaxyproject.org

(no subject)
by Ying Zhang 08 Feb '11

08 Feb '11

Hi: My name is Ying, a postdotoral associate working in Yale university. I am trying to use tophat in galaxy to analyze paired-end RNA-seq data, however, after I groomer and use tophat to analyze them, I only got an empty file. I am wondering what is the problem here. One thing I am concerned is that my files is kind of large, e.g., for each end I got a file with 20.7 gb, so totally 41.4 gb for both ends of this sample. So do you think it is because the files are too big? Also when the genome center sent me the data, they already separate the two ends into two files, so I uploaded two files for one sample, but when do tophat analysis, do I need to merge those two files into one file? do you know what is the usual parameter set up for paried-end RNA-seq analysis(with a 300 bp fragment)? Thank you very much! I really appreciate your help! Best Ying Zhang, M.D., Ph.D. Postdoctoral Associate Department of Genetics, Yale University School of Medicine 300 Cedar Street,S320 New Haven, CT 06519 Tel: (203)737-2616 Fax: (203)737-2286

2 1

Galaxy for gene expression comparison
by Martin, David A. 07 Feb '11

07 Feb '11

Hello, I am comparing RNA expression in two groups of rats, a drug treated group against a control group. There are 10 biological replicates in each group. I am unsure of how to flow this analysis through Galaxy using Tophat followed by Cufflinks/compare/diff. Should the files for each group be merged at any point? I would think they should be kept separate in order to properly account for the spread across animals. I am just a little unsure of how to group the files on galaxy, and where to differentiate biological and technical replicates. On a different note, is there a way to control the bowtie mapping parameters more closely when using tophat? Thank you for any kind of knowledge on these matters! -David Martin

5 9

Re: [galaxy-user] About NCBI refSeq id
by Jennifer Jackson 07 Feb '11

07 Feb '11

Hello Shibu, The refGene.txt table from UCSC (file from downloads or as extracted using their Table browser), contains the current RefSeq transcripts for mouse, from NCBI, if they align with BLAT to the mouse genome (most should). So the issue is likely with your input list's content. Some things to check: - are there older versions of sequences mixed in with the new (duplicates - check the ".N" versioning) - are all sequences still active (none are deleted)? - maybe not all sequences are mouse? You could explore the "Other RefSeq" track at UCSC if you want to find out about RefSeq sequences from other species, in the context of an alignment to the mouse genome. - if sequence is active, most current, mouse, and not in list - try running a quick web-BLAT at UCSC. If it doesn't align, and you cannot tell why, the best thing to do is to ask them directly why the alignment failed at genome(a)ucsc.edu. Sequence quality may be an issue (Genome or RefSeq), but they can help with the exact why. Hopefully this helps! Thanks, Jen Galaxy team ps. Next time, for data questions, please use galaxy-user(a)bx.psu.edu. Any non-confidential follow-up should also post back to the list so the entire team and subscribers can offer input/learn. On 2/4/11 9:22 AM, Shibu John wrote: > Hi Jen, > > I have a list of (36692) NCBI refSeq id in the following format. (Mouse ) > ***** > gi|10048421|ref|NM_020488.1| > gi|10048425|ref|NM_020501.1| > **** > Is there any way to get the chromosome start position of these geneID > with Galaxy? > > I tried to intersect with the "NM_" id with UCSC > "http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/refGene.txt.gz" > ******** > gi|10048425|ref|NM_020501.1| Tas2r105 NM_020501 chr6 > - 131636578 131637481 > ******** > > But this "refGene.txt" contains only 28108 id's.. > > It will be a great help that if you can help me to get the chromosome > start position of these genes. > > Thanks, > Shibu > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

1 0

Stitch MAF help
by Jennifer Jackson 07 Feb '11

07 Feb '11

fwd to galaxy-user(a)bx.psu.edu On 2/7/11 6:13 AM, Antigoni Elefsinioti wrote: > Hi, I dont know if I should sent the email to you but I am new in the > genomics field and I am kinda lost. > My problem is I want for each of the mouse chromosomes to stitch the > given MAFs and get a complete alignment. I was suggested from galaxy's > site to go to > https://bitbucket.org/james_taylor/bx-python/wiki/Home > I downloaded and installed the bx-python package, but know I dont know > which script to run > I would appreciate any help > Thanks > Anna -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org

1 0

Re: [galaxy-user] Welcome to the "galaxy-user" mailing list
by Li, Xuekun 07 Feb '11

07 Feb '11

________________________________________ From: galaxy-user-bounces(a)lists.bx.psu.edu [galaxy-user-bounces(a)lists.bx.psu.edu] On Behalf Of galaxy-user-request(a)lists.bx.psu.edu [galaxy-user-request(a)lists.bx.psu.edu] Sent: Friday, February 04, 2011 2:43 PM To: Li, Xuekun Subject: Welcome to the "galaxy-user" mailing list Welcome to the galaxy-user(a)lists.bx.psu.edu mailing list! To post to this list, send your email to: galaxy-user(a)lists.bx.psu.edu General information about the mailing list is at: http://lists.bx.psu.edu/listinfo/galaxy-user If you ever want to unsubscribe or change your options (eg, switch to or from digest mode, change your password, etc.), visit your subscription page at: http://lists.bx.psu.edu/options/galaxy-user/xuekun.li%40emory.edu You can also make such adjustments via email by sending a message to: galaxy-user-request(a)lists.bx.psu.edu with the word `help' in the subject or body (don't include the quotes), and you will get back a message with instructions. You must know your password to change your options (including changing the password, itself) or to unsubscribe. It is: naewgouf Normally, Mailman will remind you of your lists.bx.psu.edu mailing list passwords once every month, although you can disable this if you prefer. This reminder will also include instructions on how to unsubscribe or change your account options. There is also a button on your options page that will email your current password to you. This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

2 1

Usability - show vs peep, editing attributes, and histories
by Peter 04 Feb '11

04 Feb '11

Dear all, I've just been sitting down with one of our biologists who is learning to use (our local) Galaxy, and he ran into a few little issues, some of which should be fairly easy to address. This is intended as constructive feedback, and if anything is unclear please say and I'll try to elaborate. *Show data vs peep* When wanting to look at an entry in the history, he would always click on the title (which toggles the peep view), berate himself, then click on the small eye icon. This is something that I used to do when first learning to use Galaxy too. Viewing data is a very common task yet the icon is tiny compared to the name, which is the most natural thing to click on. Does this confuse most newcomers? I realise it would upset existing users, but have you considered switching this functionality? *Editing attributes (of a history entry)* Several of the history entries had automatic names set by the tools, and as a result some of them had the same name. We therefore wanted to rename these entries, via the "pencil" icon for "edit attributes". The attributes page has five (independent) blocks, each with their *own* save or action button. He edited the name, and clicked on save - Galaxy went back to the main view but nothing had happened. Why? He'd clicked on the wrong save button. The first thing I'd change is quite small: He'd clicked on the most prominent save button, the "Change data type" block save button which happened to be on the bottom of the visible screen. Part of the issue is that the "Edit Attributes" block's save button is not last, but second last. It is therefore somewhat hidden. So I'd move it below the auto-detect button to ensure it is at the end of the block. The second thing I'd suggest (and this applies to Galaxy in general) is moving the save/commit/execute buttons to the right of the frame. That way all the text and options are left aligned, but the "do it" button stands out on the right (which is a common convention in software in general - think of wizards and dialogue windows). Finally I'd suggest (assuming it is possible) making the text of any primary button (e.g. save/commit/execute button) bold to help it stand out from all the options or buttons. *Saving histories* When the user had finished one task, and was about to start another, I suggested we make a new history. There is no explicit "Save History" option (since it happens automatically), so the correct action was to click on "Create New". We were then left with two "Unnamed histories" and everything was fine - but never the less a bit nerve racking for the novice as there is no indication that the old history was saved. I would suggest if the current history is still unnamed, having a prompt along the lines of "You current history will be saved as: XXX" where XXX is the current name (default being Unnamed as now), giving them a chance to (re)name it. *Renaming current history* There is no obvious way to rename the current history from the "main" page. Currently the only way I've found to do this is go to "history options", "saved histories". I would suggest adding a rename entry under the "history options". Regards, Peter

2 2

FASTQ collapse?
by Johnson, Kory (NIH/NINDS) [C] 03 Feb '11

03 Feb '11

Hello Galaxy users, Just to follow-up on my user group question described in the list-serv e-mail just sent out. I put forth the question about FASTQ collapse, as the FASTX-toolkit by Assaf Gordon describes the supported collapse tool as follows: "FASTQ/A Collapser, Collapsing identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts)" Yet, the collapse tool in Galaxy appears to be FASTA supported only? Why am I asking? Would like to remove duplicate reads in a FASTQ file by sequence, leaving one representative unique read having the best quality line among the duplicates it was identified from. Can certainly convert FASTQ to FASTA, then collapse, but if you do not have the qual file, you cannot reconstitute a FASTQ file with actual qual scores. Any argument for or against? Or can Galaxy already do and I am missing the tool to actually use? Thanks ... best, Kory -------------------------------------------- Kory R. Johnson, MS, PhD Sr. Bioinformatics Scientist www.kellygovernmentsolutions.com Providing Contract Services For: Bioinformatics Section, Information Technology & Bioinformatics Program, Division of Intramural Research (DIR), National Institute of Neurological Disorders & Stroke (NINDS), National Institutes of Health (NIH), Bethesda, Maryland Mailing Address: NINDS/NIH Clinical Center (Building 10) Office 5S223 9000 Rockville Pike Bethesda, MD 20892 Contact Information: Phone: 301-402-1956 Fax: 301-480-3563 email: johnsonko(a)ninds.nih.gov  Green Message: Please consider the environment before printing this e-mail. Thank you. Important Message: This electronic message transmission contains information intended for the recipient only. Such that, the information contained herein may be confidential, privaledged, or proprietary. If you are not the intended recipient, be aware that any disclosure, copying, distribution, or use of this information is strictly prohibited. If you have received this electronic information in error, please notify the sender immediately by telephone. Thank you. -------------------------------------------- -----Original Message----- From: galaxy-user-request(a)lists.bx.psu.edu [mailto:galaxy-user-request@lists.bx.psu.edu] Sent: Thursday, February 03, 2011 12:52 PM To: galaxy-user(a)lists.bx.psu.edu Subject: galaxy-user Digest, Vol 56, Issue 4 Send galaxy-user mailing list submissions to galaxy-user(a)lists.bx.psu.edu To subscribe or unsubscribe via the World Wide Web, visit http://lists.bx.psu.edu/listinfo/galaxy-user or, via email, send a message with subject or body 'help' to galaxy-user-request(a)lists.bx.psu.edu You can reach the person managing the list at galaxy-user-owner(a)lists.bx.psu.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-user digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-user Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. CuffDiff gene fpkm tracking file. (Samuele Gherardi) 2. CuffDiff gene fpkm tracking file- Sorry! I sent only a part of my email (Samuele Gherardi) 3. Re: listing attributes of data input (Peter) 4. Re: CuffDiff gene fpkm tracking file. (Jeremy Goecks) 5. Re: Downloadable Galaxy Virtual Machine in VMware (Haarst, Jan van) 6. Re: Downloadable Galaxy Virtual Machine in VMware (Nate Coraor) 7. FASTQ collapse? (Johnson, Kory (NIH/NINDS) [C]) ---------------------------------------------------------------------- Message: 1 Date: Thu, 3 Feb 2011 09:53:44 +0000 From: Samuele Gherardi <samuele.gherardi(a)unibo.it> To: "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu> Subject: [galaxy-user] CuffDiff gene fpkm tracking file. Message-ID: <025DB19130DE0B43BBD868BDB9244A82C134(a)E10-MBX3-DR.personale.dir.unibo.it> Content-Type: text/plain; charset="iso-8859-1" this is an example of my CuffDiff gene fpkm tracking file. tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi XLOC_000001 - - MT-ND5 - chrM:0-16571 12484.2 12260.8 12707.7 11447 11233.1 11661 XLOC_000002 - - USP14 TSS1,TSS2,TSS3 chr18:148586-236453 16.7235 9.41244 24.0346 19.437 11.7368 27.1371 XLOC_000003 - - SMCHD1 TSS10,TSS11,TSS12,TSS4,TSS5,TSS6,TSS7,TSS8,TSS9 chr18:2719322-2728540 28.2493 17.5093 38.9892 27.2263 16.6263 37.8262 XLOC_000004 - - EMILIN2 TSS13,TSS14 chr18:2880607-2882469 3.98118 0 7.99721 4.62875 0.278519 8.97899 I this is normal, how can I find the class code of transcript listed in the CuffDiff gene expression file? thank you in advance Samuele. ------------------------------ Message: 2 Date: Thu, 3 Feb 2011 10:58:47 +0000 From: Samuele Gherardi <samuele.gherardi(a)unibo.it> To: "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu> Subject: [galaxy-user] CuffDiff gene fpkm tracking file- Sorry! I sent only a part of my email Message-ID: <025DB19130DE0B43BBD868BDB9244A82CB4C(a)E10-MBX3-DR.personale.dir.unibo.it> Content-Type: text/plain; charset="iso-8859-1" Hello everybody, I'm quite new in NGS world, I'm trying to analize dome RNA-seq data. I followed the workflow through tophat,cufflink,cuffcompare and cuffdiff I suppose everything work fine but in the Cuffdiff gene fpkm file the column Class_Code is empty and i don't know why? this is an example of my CuffDiff gene fpkm tracking file. tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi XLOC_000001 - - MT-ND5 - chrM:0-16571 12484.2 12260.8 12707.7 11447 11233.1 11661 XLOC_000002 - - USP14 TSS1,TSS2,TSS3 chr18:148586-236453 16.7235 9.41244 24.0346 19.437 11.7368 27.1371 XLOC_000003 - - SMCHD1 TSS10,TSS11,TSS12,TSS4,TSS5,TSS6,TSS7,TSS8,TSS9 chr18:2719322-2728540 28.2493 17.5093 38.9892 27.2263 16.6263 37.8262 XLOC_000004 - - EMILIN2 TSS13,TSS14 chr18:2880607-2882469 3.98118 0 7.99721 4.62875 0.278519 8.97899 I this is normal, how can I find the class code of transcript listed in the CuffDiff gene expression file? thank you in advance Samuele. ------------------------------ Message: 3 Date: Thu, 3 Feb 2011 11:05:07 +0000 From: Peter <peter(a)maubp.freeserve.co.uk> To: Freddy de Bree <freddy.debree(a)wur.nl> Cc: galaxy-user(a)lists.bx.psu.edu Subject: Re: [galaxy-user] listing attributes of data input Message-ID: <AANLkTimKXwr_9MFUdU7WS+qAPHTfRqdj+RRUKRLtstFX(a)mail.gmail.com> Content-Type: text/plain; charset=ISO-8859-1 On Thu, Feb 3, 2011 at 8:40 AM, Freddy de Bree <freddy.debree(a)wur.nl> wrote: > Dear all, > > I was wondering if there is a place within the Galaxy content (a config, an > xml file) > that gives me some handles on how to address attributes of data input. > > For example, I can get the 'file_name' of data input, by addressing this > attr > as 'input.file_name', and for example, the original name of the data file > can be addressed with 'input.name'. > > Anyone any clues where I can find this info? > > Freddy de Bree Some are given in examples on the main tool XML doc page, https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax Others I've noticed by looking at the provided XML wrappers, and/or email list questions. For example, .ext or .extension gives the Galaxy file type (e.g. fasta). Other than that, I guess you can always read the code - but I agree that a document describing this would be nice to have. Peter ------------------------------ Message: 4 Date: Thu, 3 Feb 2011 09:14:19 -0500 From: Jeremy Goecks <jeremy.goecks(a)emory.edu> To: Samuele Gherardi <samuele.gherardi(a)unibo.it> Cc: "galaxy-user(a)lists.bx.psu.edu" <galaxy-user(a)lists.bx.psu.edu> Subject: Re: [galaxy-user] CuffDiff gene fpkm tracking file. Message-ID: <B60DBE14-31BD-432D-92BB-FB7C8363A86F(a)emory.edu> Content-Type: text/plain; charset=us-ascii > > this is an example of my CuffDiff gene fpkm tracking file. > > tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi > XLOC_000001 - - MT-ND5 - chrM:0-16571 12484.2 12260.8 12707.7 11447 11233.1 11661 > XLOC_000002 - - USP14 TSS1,TSS2,TSS3 chr18:148586-236453 16.7235 9.41244 24.0346 19.437 11.7368 27.1371 > XLOC_000003 - - SMCHD1 TSS10,TSS11,TSS12,TSS4,TSS5,TSS6,TSS7,TSS8,TSS9 chr18:2719322-2728540 28.2493 17.5093 38.9892 27.2263 16.6263 37.8262 > XLOC_000004 - - EMILIN2 TSS13,TSS14 chr18:2880607-2882469 3.98118 0 7.99721 4.62875 0.278519 8.97899 > > I this is normal, how can I find the class code of transcript listed in the CuffDiff gene expression file? > Hi Samuele, Without seeing your history, it's difficult to say for certain what your problem is. However, I'd guess that the GTF file that you're providing to Cuffdiff does not have the p_id attribute. You can produce a GTF file with both tss_id and p_id attributes by running Cuffcompare and using sequence data. Thanks, J. ------------------------------ Message: 5 Date: Thu, 3 Feb 2011 16:54:14 +0100 From: "Haarst, Jan van" <jan.vanhaarst(a)wur.nl> To: "'Leon Mei'" <hailiang.mei(a)nbic.nl>, "'galaxy-user(a)lists.bx.psu.edu'" <galaxy-user(a)lists.bx.psu.edu> Cc: 'David van Enckevort' <david.van.enckevort(a)nbic.nl>, 'Rob Hooft' <rob.hooft(a)nbic.nl> Subject: Re: [galaxy-user] Downloadable Galaxy Virtual Machine in VMware Message-ID: <48B2C6E110F6CC4387AFCD2EBCCA0B3B25D12D432F(a)scomp0536.wurnet.nl> Content-Type: text/plain; charset="iso-8859-1" The download can also be done using bittorrent, torrent is available at http://www.biotorrents.net/details.php?id=136 . This might be faster, as one of the peers is in Canada. With kind regards, Jan > -----Original Message----- > From: galaxy-user-bounces(a)lists.bx.psu.edu [mailto:galaxy-user- > bounces(a)lists.bx.psu.edu] On Behalf Of Leon Mei > Sent: Tuesday, February 01, 2011 1:08 PM > To: galaxy-user(a)lists.bx.psu.edu > Cc: David van Enckevort; Rob Hooft > Subject: [galaxy-user] Downloadable Galaxy Virtual Machine in VMware > > Dear list, > > Within the Netherlands Bioinformatics Centre, we have implemented a Galaxy VM by > wrapping up the distributed version from PennState. We are also adding more easy-to- > use pipelines for Genomics and Proteomics data analysis into this server at the > moment. > > You can download the current version at: http://bet1.nbiceng.net/galaxy/ > > More documents can be found at: https://wiki.nbic.nl/index.php/Galaxy_VM > > By sharing this VM, we hope to relieve you from the normal installation and > configuration steps (sometimes can be difficult) if you want to run a local Galaxy > instance. > > If you are interested in this procedure or have questions on that, we are happy to > share our experience and scripts. > > Best regards, > Leon > > -- > Hailiang (Leon) Mei > Netherlands Bioinformatics Center (http://www.nbic.nl/) > Skype: leon_mei? ? Mobile: +31 6 41709231 > > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user ------------------------------ Message: 6 Date: Thu, 3 Feb 2011 11:37:01 -0500 From: Nate Coraor <nate(a)bx.psu.edu> To: "Haarst, Jan van" <jan.vanhaarst(a)wur.nl> Cc: "'galaxy-user(a)lists.bx.psu.edu'" <galaxy-user(a)lists.bx.psu.edu>, 'Leon Mei' <hailiang.mei(a)nbic.nl>, 'David van Enckevort' <david.van.enckevort(a)nbic.nl>, 'Rob Hooft' <rob.hooft(a)nbic.nl> Subject: Re: [galaxy-user] Downloadable Galaxy Virtual Machine in VMware Message-ID: <20110203163701.GE15147(a)bx.psu.edu> Content-Type: text/plain; charset=iso-8859-1 Haarst, Jan van wrote: > The download can also be done using bittorrent, torrent is available at http://www.biotorrents.net/details.php?id=136 . > This might be faster, as one of the peers is in Canada. This is great! I haven't checked the image out, but I'm fetching the torrent now and will leave it seeding here from PSU to help out. Thanks, --nate > > With kind regards, > Jan > > > > -----Original Message----- > > From: galaxy-user-bounces(a)lists.bx.psu.edu [mailto:galaxy-user- > > bounces(a)lists.bx.psu.edu] On Behalf Of Leon Mei > > Sent: Tuesday, February 01, 2011 1:08 PM > > To: galaxy-user(a)lists.bx.psu.edu > > Cc: David van Enckevort; Rob Hooft > > Subject: [galaxy-user] Downloadable Galaxy Virtual Machine in VMware > > > > Dear list, > > > > Within the Netherlands Bioinformatics Centre, we have implemented a Galaxy VM by > > wrapping up the distributed version from PennState. We are also adding more easy-to- > > use pipelines for Genomics and Proteomics data analysis into this server at the > > moment. > > > > You can download the current version at: http://bet1.nbiceng.net/galaxy/ > > > > More documents can be found at: https://wiki.nbic.nl/index.php/Galaxy_VM > > > > By sharing this VM, we hope to relieve you from the normal installation and > > configuration steps (sometimes can be difficult) if you want to run a local Galaxy > > instance. > > > > If you are interested in this procedure or have questions on that, we are happy to > > share our experience and scripts. > > > > Best regards, > > Leon > > > > -- > > Hailiang (Leon) Mei > > Netherlands Bioinformatics Center (http://www.nbic.nl/) > > Skype: leon_mei? ? Mobile: +31 6 41709231 > > > > _______________________________________________ > > galaxy-user mailing list > > galaxy-user(a)lists.bx.psu.edu > > http://lists.bx.psu.edu/listinfo/galaxy-user > > > > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user > ------------------------------ Message: 7 Date: Thu, 3 Feb 2011 12:51:34 -0500 From: "Johnson, Kory (NIH/NINDS) [C]" <johnsonko(a)ninds.nih.gov> To: "'galaxy-user(a)bx.psu.edu'" <galaxy-user(a)bx.psu.edu> Subject: [galaxy-user] FASTQ collapse? Message-ID: <F142C51C02C33C418E931103600D1E670648E93762(a)NIHMLBXBB03.nih.gov> Content-Type: text/plain; charset="us-ascii" Hello, Is there an option to collapse duplicate sequences in FASTQ format. I see collapse for FASTA, but where is it for FASTQ? Thank you, Kory -------------------------------------------- Kory R. Johnson, MS, PhD Sr. Bioinformatics Scientist [cid:image001.jpg@01CBC39E.D7F751F0] www.kellygovernmentsolutions.com Providing Contract Services For: Bioinformatics Section, Information Technology & Bioinformatics Program, Division of Intramural Research (DIR), National Institute of Neurological Disorders & Stroke (NINDS), National Institutes of Health (NIH), Bethesda, Maryland Mailing Address: NINDS/NIH Clinical Center (Building 10) Office 5S223 9000 Rockville Pike Bethesda, MD 20892 Contact Information: Phone: 301-402-1956 Fax: 301-480-3563 email: johnsonko(a)ninds.nih.gov P Green Message: Please consider the environment before printing this e-mail. Thank you. Important Message: This electronic message transmission contains information intended for the recipient only. Such that, the information contained herein may be confidential, privaledged, or proprietary. If you are not the intended recipient, be aware that any disclosure, copying, distribution, or use of this information is strictly prohibited. If you have received this electronic information in error, please notify the sender immediately by telephone. Thank you. --------------------------------------------

2 3

FASTQ collapse?
by Johnson, Kory (NIH/NINDS) [C] 03 Feb '11

03 Feb '11

Hello, Is there an option to collapse duplicate sequences in FASTQ format. I see collapse for FASTA, but where is it for FASTQ? Thank you, Kory -------------------------------------------- Kory R. Johnson, MS, PhD Sr. Bioinformatics Scientist [cid:image001.jpg@01CBC39E.D7F751F0] www.kellygovernmentsolutions.com Providing Contract Services For: Bioinformatics Section, Information Technology & Bioinformatics Program, Division of Intramural Research (DIR), National Institute of Neurological Disorders & Stroke (NINDS), National Institutes of Health (NIH), Bethesda, Maryland Mailing Address: NINDS/NIH Clinical Center (Building 10) Office 5S223 9000 Rockville Pike Bethesda, MD 20892 Contact Information: Phone: 301-402-1956 Fax: 301-480-3563 email: johnsonko(a)ninds.nih.gov P Green Message: Please consider the environment before printing this e-mail. Thank you. Important Message: This electronic message transmission contains information intended for the recipient only. Such that, the information contained herein may be confidential, privaledged, or proprietary. If you are not the intended recipient, be aware that any disclosure, copying, distribution, or use of this information is strictly prohibited. If you have received this electronic information in error, please notify the sender immediately by telephone. Thank you. --------------------------------------------

1 0

Downloadable Galaxy Virtual Machine in VMware
by Leon Mei 03 Feb '11

03 Feb '11

Dear list, Within the Netherlands Bioinformatics Centre, we have implemented a Galaxy VM by wrapping up the distributed version from PennState. We are also adding more easy-to-use pipelines for Genomics and Proteomics data analysis into this server at the moment. You can download the current version at: http://bet1.nbiceng.net/galaxy/ More documents can be found at: https://wiki.nbic.nl/index.php/Galaxy_VM By sharing this VM, we hope to relieve you from the normal installation and configuration steps (sometimes can be difficult) if you want to run a local Galaxy instance. If you are interested in this procedure or have questions on that, we are happy to share our experience and scripts. Best regards, Leon -- Hailiang (Leon) Mei Netherlands Bioinformatics Center (http://www.nbic.nl/) Skype: leon_mei Mobile: +31 6 41709231

3 2

CuffDiff gene fpkm tracking file.
by Samuele Gherardi 03 Feb '11

03 Feb '11

this is an example of my CuffDiff gene fpkm tracking file. tracking_id class_code nearest_ref_id gene_short_name tss_id locus q1_FPKM q1_conf_lo q1_conf_hi q2_FPKM q2_conf_lo q2_conf_hi XLOC_000001 - - MT-ND5 - chrM:0-16571 12484.2 12260.8 12707.7 11447 11233.1 11661 XLOC_000002 - - USP14 TSS1,TSS2,TSS3 chr18:148586-236453 16.7235 9.41244 24.0346 19.437 11.7368 27.1371 XLOC_000003 - - SMCHD1 TSS10,TSS11,TSS12,TSS4,TSS5,TSS6,TSS7,TSS8,TSS9 chr18:2719322-2728540 28.2493 17.5093 38.9892 27.2263 16.6263 37.8262 XLOC_000004 - - EMILIN2 TSS13,TSS14 chr18:2880607-2882469 3.98118 0 7.99721 4.62875 0.278519 8.97899 I this is normal, how can I find the class code of transcript listed in the CuffDiff gene expression file? thank you in advance Samuele.

2 1