April 2013 - galaxy-user - lists.galaxyproject.org

Regarding a cuffdiff output
by Yona Kim 08 Apr '13

08 Apr '13

Dear galaxy users Hello. I have a quick question about Cuffdiff analysis. I have obtained two SRA files and converted them to fastq files which were uploaded to Galaxy via FTP server. My analysis was followed by Fastq groomer, Tophat, Cufflinks, Cuffcompare, and eventually Cuffdiff. (Gene annotation was also downloaded from UCSC table browser in GTF format) I've downloaded gene differential expression testing, one of the output files of Cuffdiff, and viewed it in excel sheet. However, I have only zeros recorded for value_1, value_2, log2, test_stat and only ones recorded for p_value and q_value. Is it likely that I might have obtained wrong gene annotation file and caused this problem? Thank you Yona Kim Department of Genetics Rutgers University - New Brunswick Campus

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FW: Change format with "edit attributes"
by Gema Sanz Santos 08 Apr '13

08 Apr '13

Hi Peter, Thank you for your fast answer. I just want to know how can I use output files from Barcode splitter to use them into Bowtie for Illumina because I can´t see any tool to convert FASTA to FASTAQ. How can I continue with the mapping using the files from Barcode splitter? Best, Gema From: Peter Cock <p.j.a.cock(a)googlemail.com> Date: Wednesday, April 3, 2013 4:42 PM To: Gema Sanz Santos <ge2sasag(a)gmail.com> Cc: <galaxy-user(a)lists.bx.psu.edu> Subject: Re: [galaxy-user] Change format with "edit attributes" On Wed, Apr 3, 2013 at 3:40 PM, Gema Sanz Santos <ge2sasag(a)gmail.com> wrote: > Hello, > > I'm trying to change the format to the output files from Barcode splitter from > FASTA to FASTAQ so I can use them in Bowtie for Illumina. I've read that it > can be done through the edit attributes, I go to datatype and select fastaq, > save and then go to convert format and press convert but the resulting file is > 0 bytes and is not recognized by Bowtie. > > I´ve also tried to upload by copying the link and selecting fastaq as format > but in this case, I got the file shown in the picture and it is not recognized > by Bowtie again. > > > What can I do?? I don´t know how to continue because I´m not able to change > the format to fastaq! > > Thank you very much for your help in advance > > Best, > Gema > Hi Gema, There seem to be several factors confusing you here. The screenshot shows FASTA data wrongly labelled as FASTQ. The Galaxy "edit attributes" does NOT actually edit the data. There are separate tools which can convert from one format to another, which gives you a new entry in the history (another green box on the right). You can convert from FASTQ to FASTA, but doing the opposite is not possible without inventing quality scores (e.g. give everything score 30). Does that help? Peter

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Genomic Intervals Coverage: csv of 2nd dataset Identifiers
by Kumar, Charu Gupta 08 Apr '13

08 Apr '13

Hi, My question is about "operating on genomic intervals, Coverage" tool. I wanted a csv list of identifiers (c4) in the second dataset that cover each interval in the first dataset. How would I go about getting such a list? Thank you so much in advance. Best, Charu Charu Gupta Kumar, Ph.D.

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Peak Overlap Analysis, allowing space between "overlapping" peaks
by Eric Van Otterloo 08 Apr '13

08 Apr '13

Hello - I have been trying to find a solution to identify overlapping peaks between two ChIP-Seq datasets. I have used the "Intersect the intervals of two datasets" function, under the *Operate on Genomic Intervals* toolset - however, I would like to be able to specify a given distance between the peaks to still be counted as "overlapping", and this tool requires at least 1bp overlap between peaks to be counted. For example, even if two peaks are within 500bp of each other (but don't overlap) I would like to score this as overlapping and get the resulting genomic coordinates for downstream analysis. Thanks in advance for your help! Eric Van Otterloo

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(no subject)
by Davide Degli Esposti 05 Apr '13

05 Apr '13

Dear Galaxy team, I have a question about RNA analysis with the cufflinks package. I have some bam files to analyze from a SOLiD platform. Some previous tests show that these bam/sam files are different from those coming from Tophat and cufflinks cannot assemble them using a reference annotation (XS attribute lacking in spliced alignments). (see https://main.g2.bx.psu.edu/u/davide-degliesposti/h/rna-seqtest-datasetscuff…) An apparent solution is to include the reference annotation in the cuffmerge (see https://main.g2.bx.psu.edu/u/davide-degliesposti/h/rna-seqtest-datasetsapri…) or cuffcompare (see https://main.g2.bx.psu.edu/u/davide-degliesposti/h/rna-seqtest-datasetsjan-…) steps. Doing like this allowed me to run cuffdiff on my datasets without apparent technical errors. However, when I compare the list of differentially expressed transcripts (DETs), these results extremely different: using cuffcompare, I got 390 DETs and using cuffmerge I got 770 DETs, but just 60 genes are shared between the two lists. The parameters used in cuffdiff (FDR, Min Alignement counts, etc.) are the same for the two analyses. Do you have any explanation about that? I expected that cuffcompare and cuffmerge did not lead to outputs quantitatively different. Where may the source of this difference be? I thank you for your cooperation Davide --- Davide Degli Esposti, PhD Epigenetic (EGE) Group International Agency for Research on Cancer Tel. +33 4 72738036 Fax. +33 4 72738322 150, cours Albert Thomas 69372 Lyon Cedex 08 France ----------------------------------------------------------------------- This message and its attachments are strictly confidential. If you are not the intended recipient of this message, please immediately notify the sender and delete it. Since its integrity cannot be guaranteed, its content cannot involve the sender's responsibility. Any misuse, any disclosure or publication of its content, either whole or partial, is prohibited, exception made of formally approved use -----------------------------------------------------------------------

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FastQC Issue with per base nucleotide quality graph
by Tan, Justin 05 Apr '13

05 Apr '13

Hi, I am having a problem with FastQC. When I view per base quality, it gives me a strange looking graph: [cid:2f881b69-b1f8-4c44-8f23-2cf3799bd703@fasmail.harvard.edu] I am wondering it this is because of a problem with my data? None of my colleagues have seen this before. Thanks! Justin

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Call for papers for a special GCC2013 and Galaxy series in GigaScience
by Dave Clements 04 Apr '13

04 Apr '13

Hello all, I am pleased to inform you that talks presented at the 2013 Galaxy Community conference will be eligible for consideration to be published in the journal *GigaScience* and that BGI will generously cover the article processing fees for these articles. See the announcement below for details. thanks, Dave C -------------------------------- The 2013 Galaxy Community Conference (GCC2013)<http://wiki.galaxyproject.org/Events/GCC2013> and BioMed Central <http://www.biomedcentral.com/> are announcing a special thematic series in *GigaScience <http://www.gigasciencejournal.com/> *, a new journal co-published in collaboration between BGI Shenzhen<http://www.genomics.cn/en/index> and BioMed Central <http://www.biomedcentral.com/> focused on studies utilizing large-scale datasets and workflows. Galaxy<http://galaxyproject.org/> is an open, web-based platform for data intensive biomedical research allowing their growing community of users to reproduce and share analyses. All accepted oral presentations from the meeting will be eligible for consideration in the series, and working with the scientific committee<http://wiki.galaxyproject.org/Events/GCC2013/Organizers#Scientific_Committee>, peer review will be coordinated, thorough and timely. BGI has been generously covering the open-access article-processing charges<http://www.gigasciencejournal.com/about/apcfaq> for the journal’s launch, and this offer will be extended to all submissions from the 2013 conference. Covering the themes of the conference, discussion and research is considered highlighting best practice for local Galaxy installation, management and use, as well as interesting tools, data sources, or novel uses of Galaxy. Addressing many of the goals of Galaxy to enable more accessible, reproducible, and transparent genomic science, submissions can utilize a novel format, where all of the workflows, tools and supporting data can be hosted and integrated into accepted papers using independently citable digital object identifiers<http://en.wikipedia.org/wiki/Digital_object_identifier> from the journal's Giga-Galaxy server <http://galaxy.cbiit.cuhk.edu.hk/> and GigaDB database <http://gigadb.org/>. Please contact the conference organizers <gcc2013-sci(a)galaxyproject.org> or GigaScience editors <editorial(a)gigasciencejournal.com> for further information, or submit a manuscript<http://www.gigasciencejournal.com/authors/instructions/research> or conference abstract<http://wiki.galaxyproject.org/Events/GCC2013/Abstracts>, mentioning you would like to be considered in the series. The deadline for consideration for oral presentations to the meeting is 12th April, but later submissions for exceptional poster presentations (deadline 3rd May) and related work utilizing Galaxy may also be considered for the open series<http://www.gigasciencejournal.com/series> . Scott Edmunds Executive Editor *GigaScience <http://www.gigasciencejournal.com/>* -- http://galaxyproject.org/GCC2013 http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/

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Extracting sequences for transcripts from reference genome
by Lizex Husselmann 04 Apr '13

04 Apr '13

Dear Galaxy community I'm new to galaxy and would like to ask the following: I have trimmed, QC'ed my data received from Illumina HiScan SQ, paired and single end data. Mapped using Tophat, run cufflinks, cuffmerge and cuffdiff. I would like to analyze the gene_exp.diff file by extracting the significant transcripts. I've used grep "yes" to extract only the significant transcripts. From this info I have the locus start and end coordinates of each transcript for example "XLOC_000544 XLOC_000544 - chr1:12763969-12765675 C0 C4 OK 3.16487 1628.25 9.00696 -4.57022 4.8722e-06 0.00905256 yes". How can I go about to extract this information/or sequence from the reference genome. Kind regards Lizex This message is confidential and may be covered by legal professional privilege. It must not be read, copied, disclosed or used in any other manner by any person other than the addressee(s). Unauthorised use, disclosure or copying is strictly prohibited and may be unlawful. The views expressed in this email are those of the sender, unless otherwise stated. If you have received this email in error, please contact ARC Service Desk immediately. (mailto:Servicedesk@arc.agric.za) To report incidents of fraud and / or corruption in the ARC use our Ethics Hotline by: Phone number : 0800 000 604 Fax number : 0800 00 7788 Email address : arc(a)tip-offs.com Please Call me : 32840 Website: www.tip-offs.com For more information on the ARC Ethics Hotline, please visit our website at www.arc.agric.za.

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Phyloviz and problem viewing nexus and newick files
by Yvan Le Bras 03 Apr '13

03 Apr '13

Dear Galaxy users, I'm trying to view files from phylogenetics analyses in Newick or nexus formats. It seems that Phyloviz doesn't work since the last update of Galaxy. Can you inform me about this problem and the possibility to make Phyloviz working on a local instance? When I try on the main galaxy instance, I have the following error number: GURU MEDITATION: #1a7e2c6048fd4852ae09587cba0a09e8 Thank you very much for your help. Best Regards, Yvan -- ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Yvan Le Bras, PhD <°))))>< e-Biogenouest project http://www.e-biogenouest.org CNRS UMR 6074 IRISA-INRIA, Campus de Beaulieu, 35042 Rennes Cedex yvan.le_bras(a)irisa.fr

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Change format with "edit attributes"
by Gema Sanz Santos 03 Apr '13

03 Apr '13

Hello, I'm trying to change the format to the output files from Barcode splitter from FASTA to FASTAQ so I can use them in Bowtie for Illumina. I've read that it can be done through the edit attributes, I go to datatype and select fastaq, save and then go to convert format and press convert but the resulting file is 0 bytes and is not recognized by Bowtie. I´ve also tried to upload by copying the link and selecting fastaq as format but in this case, I got the file shown in the picture and it is not recognized by Bowtie again. What can I do?? I don´t know how to continue because I´m not able to change the format to fastaq! Thank you very much for your help in advance Best, Gema

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