October 2011 - galaxy-user - lists.galaxyproject.org

Problem with Cuffcompare
by Chandu Galaxy 12 Oct '11

12 Oct '11

Hello, I'm using Galaxy tool from about two months. I'm very new to this community. I ran into some problems when using the tools for NGS: RNA Analysis. I would like to get from the community. Here is the description of the problem. I've four different datasets (fastqsanger format). I ran the NGS: RNA Analysis tools like "Tophat for Illumina", "Cufflinks", "Cuffcompare". The Tophat and cufflinks tools are working fine but the cuffcompare is giveing out an error message like the below. Dataset generation errors *Dataset 57: Cuffcompare on data 20, data 23, and others: combined transcripts* Tool execution generated the following error message: Error running cuffcompare. Warning: Your version of Cufflinks is not up-to-date. It is recommended that you upgrade to Cufflinks v1.1.0 to benefit from the most recent features and bug fixes (http://cufflinks.cbcb.umd.edu) No fasta index found for ./input1. Rebuilding, please wait.. Error: sequence lines in a FASTA record must have the same length! The tool produced the following additional output: cuffcompare v1.0.3 (2403) cuffcompare -o cc_output -s ./input1 ./input2 ./input3 ./input4 Can anyone help me to figure out what the problem is? Let me know if you need more information. Thank you. -- Chandrasekhar

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Problem starting galaxy on Cygwin
by Oren Livne 12 Oct '11

12 Oct '11

Dear All, There are related posts but it is unclear from them how to resolve the following. I'm trying to start a Galaxy server on Cygwin and it fails when trying to fetch an egg relying on NumPy. Could you kindly advise how to resolve the error? This uses the Cygwin python 2.6.5. I tried to point Cygwin to the Windows python (2.7.2 in my case) but that was even worse, the Mako egg threw a KeyError: 'Mako' exception up front. Thank you so much, Oren -------- $ python --version Python 2.6.5 oren@oren-PC /cygdrive/c/web/galaxy-central $ sh run.sh --reload Some eggs are out of date, attempting to fetch... Fetched http://eggs.g2.bx.psu.edu/Mako/Mako-0.4.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Whoosh/Whoosh-0.3.18-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/Tempita/Tempita-0.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/lrucache/lrucache-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/NoseHTML/NoseHTML-0.4.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/pexpect/pexpect-2.4-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/amqplib/amqplib-0.6.1-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/WebHelpers/WebHelpers-0.2-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/docutils/docutils-0.7-py2.6.egg Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 30, in <module> c.resolve() # Only fetch eggs required by the config File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py", line 345, i n resolve egg.resolve() File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py", line 195, i n resolve return self.version_conflict( e.args[0], e.args[1] ) File "/cygdrive/c/web/galaxy-central/lib/galaxy/eggs/__init__.py", line 226, i n version_conflict r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env, egg. fetch ) File "/cygdrive/c/web/galaxy-central/lib/pkg_resources.py", line 565, in resol ve raise DistributionNotFound(req) # XXX put more info here pkg_resources.DistributionNotFound: numpy==1.6.0 Fetch failed.

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11. Question about formatting mouse (mm9) GTF (shamsher jagat) (galaxy-user Digest, Vol 64, Issue 11)
by Lozach, Jean 12 Oct '11

12 Oct '11

Illumina provides a ftp site where you can download all the files you need to use TopHat and Cufflinks: Bowtie index and gtf files are present for about 20 species. For most species, we do covered different data sources (mainly NCBI, Ensembl and UCSC) as well as different builds. This resource is called iGenomes. You should find in it the Ensembl mm9 GTF file compatible with TopHat You can find all the links here http://cufflinks.cbcb.umd.edu/igenomes.html and more information about iGenomes here ftp://ftp.illumina.com/README.txt The annotations will be updated next week and will also include BWA Index files. Regards Jean Lozach Manager, Bioinformatics Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 ------------------------------ Message: 11 Date: Wed, 12 Oct 2011 04:26:15 -0700 From: shamsher jagat <kanwarjag(a)gmail.com> To: galaxy-user <galaxy-user(a)lists.bx.psu.edu> Subject: [galaxy-user] Question about formattung mouse (mm9) GTF Message-ID: <CAN_Q6i4JS3fJUx__Cbv_H6veScTR0C3k3dLa96LFBRvk3oEcCg(a)mail.gmail.com> Content-Type: text/plain; charset="iso-8859-1" I have read in the mailing list that you have a workflow which can modify the human GTF file so that it will be compatible with Top Hat. Will it also work with Ensembl mm9 GTF or there is a different work flow. Thanks

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Question about formattung mouse (mm9) GTF
by shamsher jagat 12 Oct '11

12 Oct '11

I have read in the mailing list that you have a workflow which can modify the human GTF file so that it will be compatible with Top Hat. Will it also work with Ensembl mm9 GTF or there is a different work flow. Thanks

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tophat error
by zohra saci 12 Oct '11

12 Oct '11

Hello, I was trying to run tophat v1.3.2 on SOLID data and I have this error: zohra@bart:~/Bureau/cancer$ tophat -o /tmp/tophat_SRR036752/ -g 1 -p 4 -C /home/zohra/indexes_bowtie/humain_ SRR036752.fastq [Tue Oct 11 13:23:53 2011] Beginning TopHat run (v1.3.2) ----------------------------------------------- [Tue Oct 11 13:23:53 2011] Preparing output location /tmp/tophat_SRR036752// [Tue Oct 11 13:23:53 2011] Checking for Bowtie index files [Tue Oct 11 13:23:53 2011] Checking for reference FASTA file [Tue Oct 11 13:23:53 2011] Checking for Bowtie Bowtie version: 0.12.7.0 [Tue Oct 11 13:23:53 2011] Checking for Samtools Samtools Version: 0.1.18 [Tue Oct 11 13:23:53 2011] Generating SAM header for /home/zohra/indexes_bowtie/humain_ [Tue Oct 11 13:23:55 2011] Preparing reads format: fastq quality scale: phred33 (default) [FAILED] Error running 'prep_reads' Error: qual length (51) differs from seq length (51) for fastq record ! Can you help me. Thanks Zohra Saci

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CompleteGenomics publicly available genomes.
by Melissa A. Wilson Sayres 12 Oct '11

12 Oct '11

Is there a plan to add the 69 publicly available genomes from CompleteGenomics to the SharedData in Galaxy? http://www.completegenomics.com/sequence-data/download-data/ I am planning to do some analysis of a subset of these genomes in Galaxy (and I think many more in the future). I also think many CompleteGenomics users would be more likely to use Galaxy if the masterVar files were already available in Galaxy I just wanted to check if it was already on the list, before I uploaded them myself. Thanks, Melissa -- Melissa A. Wilson Sayres, PhD Miller Fellow University of California, Berkeley

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SNP and INDEL detection
by Gabriela Ronquillo-Lopez 11 Oct '11

11 Oct '11

Hello, I am new using Galaxy, I would like ask if it is possible to perform a SNP and INDEL analysis between two SAM files (mutant and wt) with Galaxy. If so, could anyone give a hint in how to proceed? Many thanks for your help in advance, Kind regards, Maria G.

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Re: [galaxy-user] Q about 'Compute' tool
by Russell Bell 11 Oct '11

11 Oct '11

Ian, using your chr1 500 1000 geneA . + chr1 2000 2500 geneB . - problem i was able to get chr1 500 1000 geneA . + 500.0 chr1 2000 2500 geneB . - 2500.0 Using c2 if c6=='+' else c3 in the Compute tool. See if it works for you. - Russell >Date: Mon, 10 Oct 2011 17:36:58 +0200 >From: Hans-Rudolf Hotz <hrh(a)fmi.ch> >To: Ian Donaldson <Ian.Donaldson(a)manchester.ac.uk>, Daniel Blankenberg > <dan(a)bx.psu.edu>, "galaxy-user(a)lists.bx.psu.edu" > <galaxy-user(a)lists.bx.psu.edu> >Subject: Re: [galaxy-user] Q about 'Compute' tool >Message-ID: <4E93111A.4060302(a)fmi.ch> >Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > >On 10/10/2011 04:45 PM, Ian Donaldson wrote: >> Thanks, but not quite what i need. >> >> If i start with two intervals: >> chr1 500 1000 geneA . + >> chr1 2000 2500 geneB . - >> >> I want to add via, e.g. 'Compute', the TSS position to the end of each >>line. The desired result being: >> >> chr1 500 1000 geneA . + 500 >> chr1 2000 2500 geneB . - 2500 >> >> This is because geneA is on the '+' strand and geneB is on the '-' >>strand. >> > >Hi Ian > >Have you tried > >"Filter and Sort"-> "Filter" data on any column using simple expressions > >and create two lists containing all genes on the '+' strand and alles >genes on the '-' strand. > >followed by >"Text Manipulation"-> "Cut" columns from a table > > using 'c1,c2,c3,c4,c5,c6,c2' for the list with all genes on the '+' > strand > > and > > using 'c1,c2,c3,c4,c5,c6,c3' for the list with all genes on the '-' > strand > > >and then you can create a single list again with > >"Text Manipulation"-> "Concatenate" datasets tail-to-head > > >I guess this is waht you want, isn't-it? > > >Regards, Hans > > >> Thanks, >> Ian >> ________________________________ >> From: Daniel Blankenberg [dan(a)bx.psu.edu] >> Sent: 10 October 2011 14:34 >> To: Ian Donaldson >> Cc: galaxy-user(a)lists.bx.psu.edu >> Subject: Re: [galaxy-user] Q about 'Compute' tool >> >> Hi Ian, >> >> Under Operate on Genomic Intervals, you can try the "Get Flanks" tool; >>you can request upstream, downstream, or both of your provided regions. >>Please let us know if you need additional assistance. >> >> >> Thanks for using Galaxy, >> >> Dan >> >> >> On Oct 10, 2011, at 6:35 AM, Ian Donaldson wrote: >> >> Hi, >> >> Can 'if' statements by used in 'Text manipulation'> 'Compute'? >> >> The reason is that i have a interval file of UCSC genes, i want to >>identify the TSS of each and make a new interval reflecting the TSS >>position for each gene. But because the TSS of a '-' stranded gene is >>actually the 'end' coord i want to be able to check the strand in the >>compute statement. >> >> Is this possible or is there an easier way to do this inside GALAXY? >> >> Thank you, >> Ian >> ___________________________________________________________ >> The Galaxy User list should be used for the discussion of >> Galaxy analysis and other features on the public server >> at usegalaxy.org<http://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/ >> >> >> >> >> >> ___________________________________________________________ >> 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/ > > >------------------------------ > >_______________________________________________ >galaxy-user mailing list >galaxy-user(a)lists.bx.psu.edu >http://lists.bx.psu.edu/listinfo/galaxy-user > > >End of galaxy-user Digest, Vol 64, Issue 9 >******************************************

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version tophat and cufflinks
by dongdong zhaoweiming 11 Oct '11

11 Oct '11

Hi, May I ask what is the version of TopHat and cufflinks in the galaxy? Thanks a lot! weimin zhao

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select tophat and cufflinks
by dongdong zhaoweiming 10 Oct '11

10 Oct '11

Hi, I'm a user of galaxy.As I know, when TopHat and Cufflinks are supported through Galaxy, its version is 1.1.1 and 0.9.3,respectively. But now, the present version of TopHat and cufflinks is 1.3.2 and 1.1.0, which have some improvement over the previous version. I have a RNA-Seq reads about pig and I want to assemble my transcripts using the latest version of tophat and cufflinks. I don't know the present version of tophat and cufflinks in the galaxy or galaxy test, so what should I do if the version is the same as the previous one based on my poor bioinformatics background. Thanks a lot! weimin zhao

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