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cufflinks-status-FAIL
by dongdong zhaoweiming 08 Dec '11

08 Dec '11

Hi, I used the cufflinks to assemble my SAM file, but the results showed some CUFF's status in not "OK",it's FAIL, so that means these CUFF's corresponding sequence could not used or else mean? Thanks a lot! Reards weimin zhao

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GI error/shift in the output of megablast ?
by Sandrine Hughes 08 Dec '11

08 Dec '11

Dear all, I have a trouble with the Megablast program available in NGS Mapping and I hope that you can help. Indeed, I think that there might be a problem with the table given in output, and notably a shift between the GI numbers and the parameters associated. Here are the details: I. First, what I have done : I used the program to identify the species that I have in a mix of sequences by using the following options: Database nt 27-Jun-2011 Word size 16 Identity 90.0 Cutoff 0.001 Filter out low complexity regions Yes I run the analyses twice and obtained exactly the same results (I used the online version of Galaxy, not a local one). II. Second, I analysed the data obtained for one of my sequence (1-202). The following lines are the beginning of the table that I obtained after the megablast and two lines with troubles: 1-202 312182292 484 99.33 150 1 0 1 150 1 150 2e-75 289.0 1-202 312182201 476 99.33 150 1 0 1 150 1 150 2e-75 289.0 1-202 308228725 928 99.33 150 1 0 1 150 19 168 2e-75 289.0 1-202 308228711 938 99.33 150 1 0 1 150 22 171 2e-75 289.0 1-202 308197083 459 99.33 150 1 0 1 150 10 159 2e-75 289.0 1-202 300392378 920 99.33 150 1 0 1 150 10 159 2e-75 289.0 1-202 300392376 918 99.33 150 1 0 1 150 9 158 2e-75 289.0 1-202 300392375 922 99.33 150 1 0 1 150 11 160 2e-75 289.0 1-202 300392374 931 99.33 150 1 0 1 150 21 170 2e-75 289.0 1-202 300392373 909 99.33 150 1 0 1 150 21 170 2e-75 289.0 1-202 300392371 1172 99.33 150 1 0 1 150 9 158 2e-75 289.0 ... 1-202 179366399 151762 98.67 150 2 0 1 150 46880 47029 6e-73 281.0 1-202 58617849 511 98.67 150 2 0 1 150 21 170 6e-73 281.0 III. Third, what I’ve noticed: My first problem was that among all the species identified, two were very different from the expected ones (2 last lines). So I decided to search if that could be possible for this sequence and performed independently a megablast on the NCBI with similar options. I was not able to find these two species in the results. So, I decided to check the hits identified in the table above and identified a second problem. In the table, the second column give the GI of the database hit and the third column give the length of the database hit. However, when I manually checked in NCBI the length of the GI, this one was incorrect. Indeed, for the GI 312182292, the length should be 580 and not 484. By checking different lines, I noticed that the length that is given for a GI corresponds to the length of the GI-1. As you can see in the above table, some GI are consecutive (300392376, 300392375,...). When checking the length of 300392376 in NCBI, I should have 920. But when I checked 300392375, I found 918. And this was true for the following lines : 300392374 give normally 922 and 300392373 give 931... My conclusion at that point was that there is a shift of –1 between the GI and the other parameters of the line (indeed the parameters for the remaining columns are in agreement with the length of the GI-1). However, that’s not always true.... For some GI given in the table (for example, the two last lines), if we check the parameters of the GI-1, the parameters are completely different... So, I suppose that there is a problem in the GI sorting during the megablast but I’m not able to clearly define the problem. IV. Fourth, confirmed with an other dataset In order to be sure that the problem was not linked to my data or my process, I asked a colleague to do a megablast on independent data. The conclusions were similar to mine : a shift in the GI given in the table and the parameters associated on the same line, that most of the time but not always, correspond to GI-1. Can you confirm that there is a problem with the output of the megablast available in Galaxy ? If yes, do you think there is a way to fix it ? Thanks a lot, Sandrine

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FASTQ Groomer before BWA mapping ?
by Praveen Raj Somarajan 08 Dec '11

08 Dec '11

All, I'm wondering why do we need to convert Illumina FASTQ into sanger using FastQ Groomer before mapping with BWA in galaxy. The lastest version of BWA itself added -I option to use Illumina data directly. What's your opinion on this? Secondly, I found that "Map with BWA for Illumina" uses -I option in the commandline during execution, even for sanger formatted reads. How does it impact the results? Thanks, Raj ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD

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To post to list
by Rose Iszati bte. Ismet 08 Dec '11

08 Dec '11

rose_ismet(a)yahoo.com

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TopHat
by Jennifer Jackson 07 Dec '11

07 Dec '11

Hello Tao, The tools in the group "NGS: Picard (beta) -> QC/Metrics for sam/bam" can generate statistics, in particular the tool SAM/BAM Alignment Summary Metrics. Another choice is "NGS: SAM Tools -> flagstat". If more statistics are needed, then starting with the original FASTQ and the mapping result SAM file, the tools in "Text Manipulation", "Filter and Sort, and Join", and "Subtract and Group" can be used in custom combinations. This question was almost missed. I was able to locate, format, and send as a new thread to the appropriate mailing list. Hopefully this reply helps or you have already found the tools above. Please help us to track new questions and provide prompt help by sending tool and data questions: 1 - to either galaxy-user(a)bx.psu.edu or galaxy-dev(a)bx.psu.edu, which are best for most questions. sending to galaxy-bugs(a)bx.psu.edu is mainly reserved for UI bug reports (green bug icon for failed datasets) or for sending shared links to private data. http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions 2 - with the "to" as the mailing list address "galaxy-user(a)bx.psu.edu". When a brand new question is sent with the mailing list as a "cc", it is not tracked. 3 - when a new question is sent as a reply to an earlier thread with a new subject line, it is not tracked. start a new thread for new questions with new subject lines. 4 - please use "reply-all" if you would like more assistance about the same subject to keep the thread consistent for the user community. Thank you for your help with this! Best, Jen Galaxy team Peng, Tao wrote: > Hi jen, after I did TopHat analysis of groomed FASTAQ data, how can I > find information on how many total reads went into TopHat? How many > reads were removed? How many unique hits to reference genome? > > I was trying to prepare a table for presentation and realize that I > could NOT find the information in my GALAXY account? > > Thanks, > > tao > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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Random Intervals ?
by Vincent Joseph Lynch 07 Dec '11

07 Dec '11

To Whom It May Concern, I am curious if there is a tool within Galaxy to generate a set of random intervals from a particular genome similar to the "Random Intervals" tool within the ENCODE tools? I am using the "Aggregate datapoints" tool to get phastCons conservation scores for peaks from ChIP-Seq data. I would like to compare these scores to a random expectation so would like to be able to use a Random Intervals-like tool to generate a set of random positions to compare to the experimental set. Best, Vinny Vincent J. Lynch, Associate Research Scientist Department of Ecology and Evolutionary Biology & Yale Systems Biology Institute Yale University "There is a grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that whilst this planet has gone on cycling according to the fixed laws of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." -C. Darwin, 1859

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Question re: Quota not re-setting after data deletion
by Mcgowen, Michael 07 Dec '11

07 Dec '11

Hello, I'm using the Galaxy Main --I was trying to groom data that I had uploaded at about 11 AM EST and Galaxy informed me that I had met my quota. Indeed it said that my quota was 98% full, but my history (my only one) said that I had about 13 Gb-- I deleted everything in my history in order to start fresh, but it still keeps saying my disk is 98% full every though my history has 0 bytes. At the moment, I have nothing in my history, but it is still saying my disk is 98% full. How do I reset the quota to 0 if not by deleting data? Michael R. McGowen, Ph.D. Postdoctoral Research Fellow Molecular Evolution Laboratory Center for Molecular Medicine and Genetics Wayne State University School of Medicine 3240 Scott Hall 540 E. Canfield St. Detroit, MI 48201 USA 313-577-0086 mmcgowen(a)med.wayne.edu http://homopan.wayne.edu/people/mmcgowen.html

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Re: [galaxy-user] Uploading Genome from Ensembl
by Jennifer Jackson 06 Dec '11

06 Dec '11

Hello Sheena, It is odd that this particular genome exists in two versions, with different content, for the same release number/date. Ensemble will update annotation with new releases, but not the reference genome itself unless they also increment the genome build number. The Zebrafish project page at Ensembl states that UCSC has the latest release, meaning that the genome labeled as "Zebrafish Jul. 2010 (Zv9/danRer7) (danRer7)" in Galaxy is expected to be the same as one would create after combining the files in their download area: http://uswest.ensembl.org/Danio_rerio/Info/Index But, if there are known differences (perhaps you want different masking or haplotypes/chrY PAR inclusion/exclusion), then combining the data can occur prior to upload into Galaxy or after (both invoke a similar tool): -- If prior, using unix and the shell "cat" command is one option. -- If after, then load all chromosomes into your history and use the tool "Text Manipulation -> Concatenate datasets tail-to-head". Best regards, Jen Galaxy team On 12/6/11 2:31 PM, Scroggins, Sheena wrote: > Thanks for responding. I would like to upload the genome to Galaxy, but I'm not sure how to combine all the fa files into one file. The Zebrafish genome from Ensembl comes in 27 separate .fa files. How do I combine these so that when I upload them to Galaxy, I can use the whole genome as my reference genome? > > Thanks, > Sheena > > -----Original Message----- > From: Jennifer Jackson [mailto:jen@bx.psu.edu] > Sent: Tuesday, November 08, 2011 6:58 AM > To: Scroggins, Sheena > Cc: galaxy-user(a)bx.psu.edu > Subject: Re: [galaxy-user] Uploading Genome from Ensembl > > Hello Sheena, > > If you concern with using the UCSC version of the database has to do with the chromosome naming and downstream Cufflinks analysis using Ensembl's reference GTF files, please see #5 on our FAQ, which demonstrates how to modify an Ensembl GTF file to be compatible with the UCSC chromosome naming (slight changes may be needed for each particular > genome): > http://main.g2.bx.psu.edu/u/jeremy/p/transcriptome-analysis-faq > > If there is another reason, please know that custom reference genomes (in fasta format) can be uploaded using FTP following this method: > http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP > > Hopefully this helps, > > Best, > > Jen > Galaxy team > > On 11/4/11 2:50 PM, Scroggins, Sheena wrote: >> How do I upload the Zebrafish genome from Ensembl to my user history >> in Galaxy? I'm trying to map my RNA-Seq data using TopHat and need to >> map it to the Ensembl version of ZFv9, but Galaxy only has the UCSC >> version built in. The Ensembl version is slightly different. >> Thanks, >> Sheena >> >> >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of Galaxy >> analysis and other features on the public server at usegalaxy.org. >> Please keep all replies on the list by using "reply all" in your mail >> client. For discussion of local Galaxy instances and the Galaxy >> source code, please use the Galaxy Development list: >> >> http://lists.bx.psu.edu/listinfo/galaxy-dev >> >> To manage your subscriptions to this and other Galaxy lists, please >> use the interface at: >> >> http://lists.bx.psu.edu/ > > -- > Jennifer Jackson > http://usegalaxy.org > http://galaxyproject.org/wiki/Support > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support

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bed file to gene list
by Dr Chris Futtner, Ph.D. 06 Dec '11

06 Dec '11

Can anyone point me to a good workflow to convert my ChIP-seq data intervals to gene names. My peaks fall both within genes and within intergenic areas. Thanks, Chris Christopher Futtner, Ph.D. Dept. of Surgery Duke University Durham, NC 27710 email: christopher.futtner(a)duke.edu phone: 919-684-1183

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How to select line with chr1?
by Di Nguyen 06 Dec '11

06 Dec '11

Hi all, I have a a bed file that I would like sort for chromosome 1 ONLY? Would you tell me the syntax to "select" lines that are chromosome 1 only instead of 1 or 10,11-19? Thank you very much, Di Nguyen U of Washington

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