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Download multiple files from history
by Adhemar 02 May '12

02 May '12

Hi, I'm trying to download multiple files from a given history but I couldn't figure out how to do it. Is there a way? Thanks, Adhemar

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Question about Samtools filter in Galaxy
by shamsher jagat 01 May '12

01 May '12

I have a sam file after running BWASW and want to extract unique (alignments that are aligning once to genome) from this sam file. I read in other posts that I may be able to use Sam tools> filter Sam option to filter the said flag on wise flag. However I could not find whether I have to use default setting of column 2? when I use option of add flags there are different options for pair reads, however my data is single reads. So exactly single read alignments sam file how we extract unique reads. Am I missing something. I can also share history in order to explain my point if required. Thanks Kanwar

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Mappability
by Brown, Stuart 01 May '12

01 May '12

I want to make an intersection between a few hundreds of genomic intervals (predicted translocation sites from SVDetect) and low mappability regions in genomes (we are working with mm9 right now). UCSC has an excellent mappability track that exactly matches our sequencing data (50 bp kmers), but it seems very difficult to get that data into Galaxy. I want a BED format that summarizes intervals of low mappability (ie. less than 0.5 on the scale used by UCSC). The UCSC Table Browser has a limit of 10M lines, which seems to give just part of chromosome 1. It will be very messy to try to get the whole genome bit by bit using this method and then stitch it back together using some sort of concatenation. UCSC Help suggests downloading the mappability data for the whole genome as a bigwig formatted file, then convert to BED. I gave this a try, but we get a 4 GB file, with intervals of just one or two base pairs. Again, lots of work to get back to the nicer BED that I could make with the UCSC tools over smaller genomic regions. Also, super-painful to upload this huge file to Galaxy, and unhappy trying to write my own parsers to filter and smooth this file. Any other suggestions? Maybe someone else knows where to find a mappability file (for mm9) that has nice intervals in a Galaxy compatible format. —Stuart Brown

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May 2012 Galaxy Update
by Dave Clements 01 May '12

01 May '12

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subtract
by Xianrong Wong 30 Apr '12

30 Apr '12

Hello, I am using the subtract (whole dataset) tool. I converted my fastq file to tabular with 2 columns: 1. Identifier and 2. sequence. I then "selected (a few) lines that match an expression" from this initial tabular file and am trying to get a final dataset that is devoid of reads with the few selected lines - thus I subtract the dataset of selected lines from the initial dataset. This tool works with I am performing the workflow on a relatively small file (1/50 the size of a whole sequencing experiment) but repeatly fails when I input the full fastq file. Any idea why this is so? Jose

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suggestion to change cuffdiff -c "Min alignment count" default to author's value of '10'
by Kevin Silverstein 30 Apr '12

30 Apr '12

Hi Galaxy Developers, This is regarding the wrapper for cuffdiff and the -c parameter for "Min alignment count". We noted that Galaxy's default value is set to 1000. In our experience, setting this parameter that high yields drastically different results from the ones obtained with the author's original default value of c = 10. The -c parameter is defined as: -c/--min-alignment-count <int> The minimum number of alignments in a locus for needed to conduct significance testing on changes in that locus observed between samples. If no testing is performed, changes in the locus are deemed not signficant, and the locus' observed changes don't contribute to correction for multiple testing. The default is 10 fragment alignments. We have found that the value entered will require that at least this number of fragment alignments be found for *each* sample (or at least each condition) in order for the locus to be tested for differential expression. Although one could save themselves a lot of locus comparisons (and hence take a much smaller hit for multiple hypothesis testing) if he/she were to raise this threshold, this will screen out the most desirable differentially expressed genes - specifically those that are not expressed at all in one condition but highly expressed in the other condition. The attached image has a real example of a gene that was counted as differentially expressed (as it should have been) with '10' but was not even tested at '100' nor '1000'. -Kevin Silverstein

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Tophat mapping error
by 杨继文 27 Apr '12

27 Apr '12

Hi all, I got the following error infomation during Tophat mapping An error occurred running this job: Job output not returned by PBS: the output datasets were deleted while the job was running, the job was manually dequeued or there was a cluster error. Please let me know what's wrong. Help will be appreciated. Thanks Jiwen

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bwa/bowtie not running
by Furey, Terry 27 Apr '12

27 Apr '12

Hi- I'm having trouble getting bwa to run on the main server. It seems stuck in the "waiting to run" state. I have tried changing the assembly to align to, and have tried re-running a previous workflow that ran fine a couple weeks ago. I even tried running bowtie, and that seems stuck. Is something wrong with the NGS server? Other NGS jobs (FastQC, filters, grooomer) seem to be fine. Thanks, Terry

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Cufflinks jobs in queue
by Scroggins, Sheena 27 Apr '12

27 Apr '12

Hi, My cufflinks jobs sat in the queued state for 12+ hours so I restarted them this morning. They've been in the queued state now for about 2-3 hours. Any idea why? Here's a link to my history: https://main.g2.bx.psu.edu/u/sheenams/h/clone-of-s1jaf13mir-active-items-on… Thanks Sheena __________________________________________________ Sheena Scroggins Post Masters Research Associate-Bioinformatics Pacific Northwest National Laboratory

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Chicken reference genome
by Nicholas Beckloff 27 Apr '12

27 Apr '12

Dear Galaxy, I noticed upon uploading a FASTQ file that the ICGSC version of the 2011 November Chicken genome is available. Why is this not available for use with the tools? Also, is this available for download? -- Nicholas Beckloff, PhD Genomics Core Laboratory Director Department of Genetics and Genome Sciences Case Western Reserve University 2109 Adelbert Road BRB 646 Cleveland, OH 44106 phone: 216-368-2791 fax: 216-368-3432 http://genomics.case.edu email: nmb64(a)case.edu

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