Re: [galaxy-user] 'Draw quality score Boxplot' error
Caroline, I've had this problem before and find that although the job 'fails', the boxplot is actually created. If you click on the 'eye' in the boxplot history item, you should still be able to see and save your plot. Regards, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601 On 28/11/2011 16:21, Avik Datta reach4a...@gmail.com wrote: Hi Caroline, Try to change the default font of gnuplot http://www.gnuplot.info/faq/faq.html#SECTION0009 On Thu, Nov 24, 2011 at 3:35 PM, Caroline Proux k...@pasteur.fr wrote: Hi,I have illumina ChipSeq data and I want to use the Draw quality score Boxplot I run thequality format converter (ASCII numeric). But the Draw quality score Boxplot do an error An error occurred running this job:Could not find/open font when opening font arial, .. where is my problem? thank you so much Caroline Proux ___ 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/ -- Avik Datta ___ 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/
Re: [galaxy-user] Creating or Downloading GTF files for use with Cuffcompare
Hello Joe, Have you found a way to convert microbial genomes from one of the formats available on Genbank to .GTF files? We are having similar issues with sequenced Prochlorococcus genomes, as well as with some of our own in-house bacterial genomes. Thanks Daniel On 20/10/2011 21:17, Joe Harrison wrote: Hello Olivier, Emilie and the Galaxy community - I have run into a similar problem with my RNA-seq analysis, in that I can run the analysis up to the point of Cufflinks producing a list of FPKM values for my genome of interest (in this case, Staphylococcus aureus strain Newman). However, I cannot find a place to download a compatible .GTF file with the reference annotation. Would you or anyone else in the community know of tool or database where .GTF files could be created from another input file (such as GFF3), or better yet, just downloaded? As for possibilities with file conversion, most microbial genomes are available from NCBI in a variety of formats (but not GTF). For S. aureus Newman, these files can be found at the following link: ftp://ftp.ncbi.nih.gov/genbank/genomes/Bacteria/Staphylococcus_aureus_Newman_uid18801 Many thanks for your help! Joe --- Joe J. Harrison Senior Fellow Department of Microbiology University of Washington 1705 NE Pacific Street, HSB J181 Seattle, WA USA 98195 On 10/20/2011 11:26 AM, Emilie Chautard wrote: Hi Olivier, Did you try to run Cuffcompare (part of Cufflinks) on your results? According to the Cufflinks manual (http://cufflinks.cbcb.umd.edu/manual.html): Cufflinks includes a program that you can use to help analyze the transfrags you assemble. The program cuffcompare helps you: - Compare your assembled transcripts to a reference annotation [...] In the Galaxy version of Cuffcompare, I think that you can provide a reference annotation file using "Use Reference Annotation:", which will be compared to your results with Cufflinks. It makes an "union" of the transcripts obtained with Cufflinks with the annotation file (both in *.gtf format). You can then obtain a transcript identifier for those already annotated. It also provides a class code for the transcripts, which can inform about a potential isoform for example. Hope this helps. Emilie -- Emilie Chautard, PhD Postdoctoral Fellow Ontario Institute for Cancer Research MaRS Centre, South Tower 101 College Street, Suite 800 Toronto, Ontario, Canada M5G 0A3 Tel: 416-673-8518 Toll-free: 1-866-678-6427 www.oicr.on.ca Message: 7 Date: Thu, 20 Oct 2011 15:12:45 +0200 From: GANDRILLON OLIVIER olivier.gandril...@univ-lyon1.fr To: "galaxy-u...@bx.psu.edu" galaxy-u...@bx.psu.edu Subject: [galaxy-user] Names for genes in RNA-Seq analysis Message-ID: cac5eaed.8e99%olivier.gandril...@univ-lyon1.fr Content-Type: text/plain; charset="windows-1252" Hello I am using Galaxy to analyse RNA-seq libraries made from chicken cells. I just groomed my sequences, passed them through TopHat and then Cufflinks. This worked well and in the end I get a list of genes and their respective FPKM values. My only problem is that the names of the genes do not appears in the listing, they are simply reference as "CUFF.1, CUFF.2, " etc? Could you please tell me how I could obtain gene names? (I went through the FAQ and could not get the answer). Sincerely Olivier ___ 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/ ___ The Galaxy User list should be used for the
[galaxy-user] Chip-seq data
Hi, I have illumina ChipSeq data in txt format with this structure: @HWI-EAS225:8:1:1:58#0/1 NAGAGTGCCCGGGTTCAGTTCTCAGCACCCATGTGG +HWI-EAS225:8:1:1:58#0/1 DMSSUSSTTTUTSRQRTTTSSSUS @HWI-EAS225:8:1:1:1803#0/1 NCCATGGGAAGAGCTGGGCAGGCGGGCCGAGCGAAG +HWI-EAS225:8:1:1:1803#0/1 DLSTTSKOUTRRTTSSSSRPNNTOJOTSSRTB @HWI-EAS225:8:1:1:1547#0/1 NAGGGGTGGGACTGGCACTTGCCTCTACCAGC +HWI-EAS225:8:1:1:1547#0/1 DLVVVTPTUVVWVVUVVUWVVVWWWVVV Can I convert into Fastq format?If so, how can I? Furthermore, after using Map with Bowtie for Illumina, how can I use MACS (Model-based Analysis of ChIP-Seq) if I have two files for IP samples and two files for Control samples? Thank you so much. Giuseppe ___ 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/
Re: [galaxy-user] Unable to run SICER or Find Peaks
Hi AP, Please keep all replies on list, this will allow the community to assist and benefit from these correspondences. SICER requires BED input. To go from BAM to BED: 1.) Convert BAM to SAM 2.) Convert SAM to Interval (Convert SAM to interval) 3.) Convert interval to BED(6+). This can be done by implicitly (by selecting the Interval dataset, which will be marked with '(as bed)' in the SICER input box) or by clicking on the pencil icon and explicitly converting uder the section Convert to new format. Please let us know if we can provide additional assistance. Thanks for using Galaxy, Dan On Nov 29, 2011, at 1:23 PM, Anupam Paliwal wrote: Hi Daniel, Thanks for your kind attention and advice. I have followed the following workflow: I aligned my query sequences to the reference genome using Bowtie; the Bowtie aligned SAM file was subjected to filter-SAM before converting it to BAM. I have re-BAM-to-SAM converted the BAM-file before subjecting it to pileup. However, now I do have the Input format file (after pileup of SAM) but am unable to convert it to BAM format to be able to submit it ti SICER. Please see if you can suggest how to convert the Input files back to BAM. I have tried changing directly through edit-attributes, but it shows error. AP Hi AP, SICER requires BED formatted input with at least 6 columns (for strand information). You can convert your BAM files into SAM and then into interval and BED format. Once you have your input in the BED (6+) format, you should be able to use these tools. Please let us know if we can provide additional information. Thanks for using Galaxy, Dan On Nov 23, 2011, at 12:26 PM, Anupam Paliwal wrote: Hi, I want to use SICER or Find Peaks for peak calling on GALAXY. I am using my aligned ChIP-seq tag .BAM files. However for both the tools the history is unable to pick the Bowtie-ligned SAM to BAM converted files. On the other hand, using MACS the same files are working nicely for peak calling. Thanks, AP ___ 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/ ___ 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/
Re: [galaxy-user] Patch for better FASTQ description handling
On 19/10/11 23:31, Daniel Blankenberg wrote: Sorry for the delay. I did try the patch out shortly after you contributed it, but it caused the functional to fail. I was able to fix the issue and allow the existing tests to start passing, but I've been bogged down lately and haven't been able to perform a more thorough review of the code. If you could provide tests with files (e.g. for the tools affected) that test the new functionality, that would be a great help. Hi Dan, I finally addressed your comments. See the updated pull request: https://bitbucket.org/galaxy/galaxy-central/pull-request/8/paired-end-code-mishandles-description-of Best, Florent ___ 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/
Re: [galaxy-user] mapping tags
Hello Soetkin, Is your concern that the sequences will be in FASTA format (without quality scores) instead of FASTQ format? If so, the Galaxy tool NGS: QC and manipulation - Combine FASTA and QUAL into FASTQ can create placeholder quality values in a FASTQ file appropriate for use with NGS mapping tools. Hopefully this helps. If you would like further help, please explain the issue in more detail and consider sending a small sample of the data pasted into the email (10 or so entries) if that is relevant. For reference: http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions Thanks for using Galaxy! Jen Galaxy team On 11/15/11 1:56 AM, Soetkin Versteyhe wrote: Dear all, I would like to map (e.g. with Bowtie) collapsed sequences (tags) instead of individual sequence reads. Does anyone know if this is possible in Galaxy? Thank you in advance. Best regards, *Soetkin Versteyhe, PhD** *PostDoc** * University of Copenhagen *Faculty of Health Sciences *The Novo Nordisk Foundation* *Center for Basic Metabolic Research* Integrative Physiology Blegdamsvej 3B * *2200 København N Denmark* ** *PHONE +45 35337116* *_soetkin.verste...@sund.ku.dk__ _http://sund.ku.dk http://metabol.ku.dk http://metabol.ku.dk/* ** * ___ 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 ___ 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/
