- galaxy-user - lists.galaxyproject.org

Combining two workflows into one
by Innocent Onsongo 19 Mar '12

19 Mar '12

Galaxy Team, I would like to create a workflow by combining portions of two different workflows. How do I do this in Galaxy? Thanks, Getiria Onsongo

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Dear Galaxy Developer, where is the "history/workflow" file stored in the local machine?
by 杨晨 18 Mar '12

18 Mar '12

Dear Galaxy Developer, where is the "history/workflow" file stored in the local machine? I mean the real file store in the disk instead of browser access. Thanks and Best regards -- Yang Chen Room 635, No.41 Building,320 Yueyang Road Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai,P.R.China Post Code:200032 Tel: 86-21-54921375

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Dear Galaxy Developer, where is the "history/workflow" file stored in the local machine?
by 杨晨 18 Mar '12

18 Mar '12

Dear Galaxy Developer, where is the "history/workflow" file stored in the local machine? Best regards -- Yang Chen Room 635, No.41 Building,320 Yueyang Road Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai,P.R.China Post Code:200032 Tel: 86-21-54921375 -------- Forwarding messages -------- From: yangchen(a)sibs.ac.cn Date: 2012-03-18 23:38:08 To: galaxy-user(a)bx.psu.edu Subject: Dear Galaxy Developer,where is the "history/workflow" flow stored in the local machine? Dear Galaxy Developer, where is the "history/workflow" flow stored in the local machine? Best regards -- Yang Chen Room 635, No.41 Building,320 Yueyang Road Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai,P.R.China Post Code:200032 Tel: 86-21-54921375

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Dear Galaxy Developer, where is the "history/workflow" flow stored in the local machine?
by yangchen＠sibs.ac.cn 18 Mar '12

18 Mar '12

Dear Galaxy Developer, where is the "history/workflow" flow stored in the local machine? Best regards -- Yang Chen Room 635, No.41 Building,320 Yueyang Road Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai,P.R.China Post Code:200032 Tel: 86-21-54921375

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wig file conversion
by Horvath, Lindsay 17 Mar '12

17 Mar '12

I am a PSU student at the College of Medicine. I have minimal bioinformatics and computer programing background. I was introduced to galaxy during televisied genomics course. I believe I am using galaxy on the cloud. I am trying to display ChIP-CHIP data on UCSC. I have downloaded the gff file (attached; NCBI/GEO # GSM413116) and uploaded it into galaxy (using get data; upload file). The initial publication converted gff file to wig file for upload into UCSC. I could not find this function in Galaxy so I tried converting to bed file instead (convert formats; gff-to-bed). When I do this and upload into UCSC I do not get the peak hight (score difference) at each site (column 6 of gff file; score--which appears to convert to all 0s in bed file), only the locations are annotated but not the score. Is there something I am doing wrong in the conversion to a bed file or alternatively is there a way to convert the intial gff file into a wig file? Any help would be greatly appreciated! Thanks, Lindsay Horvath

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fastq-MCF
by Benoît REMENANT 17 Mar '12

17 Mar '12

Hi all, Does someone know fastq-MCF? We are relatively newbies in analysing RNAseq results, and we would like to use the fastq-MCF program to trim our illumina sequences (based on quality score and adapters sequences) while keeping paired reads synchronized. Unfortunately, there are some parameters we did not understand, like -s (log scale for clip pct to threshold) and -t (% occurrence threshold before clipping). Does anyone can explain us what these parameters mean? Or when I can found useful information? And do you think we have to unable the PF filtering (and why)? Thank you very much in advance if someone can help us. Benoit

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Re: [galaxy-user] Read Length Distribution
by Jennifer Jackson 16 Mar '12

16 Mar '12

Hello, Other types of statistics can be generated with the "Join, Subtract and Group -> Group" tool, by adding an additional file manipulation. First run "Compute sequence length". Next run "Add column to an existing dataset" and set this to be the same value for all rows, "1" or something else simple. Nest, run "Group", with a group on the column containing the "Add column" value, and then click on "Add new Operation". Set "Type" to be "Mode" and "On column" to be the the sequence length. Very large files, usually when run with multiple operations, are occasionally to too large to run with this tool on the public main Galaxy instance. If this occurs, the first option is to simplify the query. If that doesn't work, then moving to a cloud instance would be the recommendation. Good luck with your project, Jen Galaxy team On 3/15/12 3:17 PM, Elad Firnberg wrote: > Hi Jen, > > Thank you, this was very helpful. Is there a way to get some more > statistical information such as the mode of read lengths? The summary > statistics tool only seems to provide the mean. > > Thank you, > Elad > > > On Thu, Mar 15, 2012 at 3:02 PM, Jennifer Jackson <jen(a)bx.psu.edu > <mailto:jen@bx.psu.edu>> wrote: > > Hi Elad, > > Start with the tool "FASTA manipulation -> Compute sequence length" > to generate a length value for each sequence. > > Next, use "Statistics -> Summary Statistics for any numerical > column" on the result to generate specific R function statistics > (see the tool form for which and how to enter the expression). > > To visualize the distribution, use "Graph/Display Data -> Histogram > of a numeric column". > > Hopefully this helps. > > Best, > > Jen > Galaxy team > > > On 3/15/12 9:24 AM, Elad Firnberg wrote: > > Hi, > > Is there a tool or easy way to obtain a read length distribution > on a > set of 454 reads in fasta format? I can't seem to find such a > tool in > Galaxy. > > Thank you, > Elad > > > > > > _____________________________________________________________ > 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 > <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/ > > > > > -- > Chemical and Biomolecular Engineering > Johns Hopkins University > 3400 N. Charles St. Baltimore, MD 21218 > Tel# (410) 516-3937

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Read Length Distribution
by Elad Firnberg 16 Mar '12

16 Mar '12

Hi, Is there a tool or easy way to obtain a read length distribution on a set of 454 reads in fasta format? I can't seem to find such a tool in Galaxy. Thank you, Elad

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Question about aaChange tool.
by Maha Al Kahtani 15 Mar '12

15 Mar '12

Hello, Recently i have used galaxy to find corresponding amino acids to a list of SNPs that i have. i used aaChange tool from the tool panel for this purpose. After obtaining the result i checked the correctness of this results by searching dbSNP for randomly chosen SNPs. however, some of those SNPs mapped to incorrect amino acid, For example, The SNP( rs11549096), was mapped by Galaxy to the change ( Asp:Tyr/His, ) , Searching the dbSNP for this SNP Shows that the Change should be Asp :Asn and the link for this SNP in the dbSNP is : http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?searchType=adhoc_searc… So, the reference is correct in all cases i searched (more than a thousand), the position of change in the aa is correct, *but* the alternative aa is not correct in all cases. What causes this mistake, and how to solve this problem? Note: my list contains hundreds of thousands of SNPs, so, i can not check each one of them. prompt response is appreciated, Best Regards, Maha

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Tophat error
by David Matthews 14 Mar '12

14 Mar '12

Hi, JUst running a TopHat job which returned the following error: Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect /local/tmp5Ywx45/dataset_942 > ./tophat_out/tmp/dataset_942.fa [Tue Mar 13 12:45:08 2012] Checking for Bowtie Bowtie version: 0.12.7.0 [Tue Mar 13 12:45:08 2012] Checking for Samtools Samtools Version: 0.1.18 [Tue Mar 13 12:45:08 2012] Generating SAM header for /local/tmp5Ywx45/dataset_942 format: fastq quality scale: phred33 (default) [Tue Mar 13 12:45:21 2012] Preparing reads left reads: min. length=56, count=29523921 right reads: min. length=56, count=29543412 [Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 with Bowtie [Tue Mar 13 13:45:26 2012] Processing bowtie hits [Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against dataset_942 with Bowtie [Tue Mar 13 15:37:46 2012] Processing bowtie hits [Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against dataset_942 with Bowtie (1/2) [Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against dataset_942 with Bowtie (2/2) [Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping Traceback (most recent call last): File "/gpfs/cluster/isys/galaxy/Software/bin/tophat", line 3063, in <module> sys.exit(main()) File "/gpfs/cluster/isys/galaxy/Software/bin/tophat", line 3029, in main user_supplied_deletions) File "/gpfs/cluster/isys/galaxy/Software/bin/tophat", line 2681, in spliced_alignment [maps[initial_reads[left_reads]].unspliced_bwt, maps[initial_reads[left_reads]].seg_maps[-1]], TypeError: list indices must be integers, not str Does anyone know what this kind of error is? Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 D.A.Matthews(a)bristol.ac.uk

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