- galaxy-user - lists.galaxyproject.org

BED to BAM conversion in Galaxy
by shamsher jagat 04 Oct '11

04 Oct '11

Is it possible to use some tool in Galaxy to convert BED file to Bam/ sam file. In other word do we have Bed tools or other option in Galaxy Thanks

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extracting 18S rRNA sequence
by Adam Stell 04 Oct '11

04 Oct '11

So I am new to Galaxy. Is there a way to search for 18S rRNA sequences in my metagenomes?

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Deletions
by Laura Reinholdt 04 Oct '11

04 Oct '11

I have a DNA seq data set from mouse genome that is heterozygous for a known 15 bp deletion. The deletion is listed in the SAM tools pileup: mapping quality = 690, SNP quality =690, mapping quality =52, coverage = 62, 11 reads span the deletion, 52 reads are reference. When I use SAM tools ‘filter pileup on coverage and SNPs’, this deletion is filtered out. I’m using the default settings for the filter: coverage=3, quality cap=60 (is this the Phred quality score or is it the Phred quality coefficient?). Does anyone whether this deletion is filtered out simply because it’s a deletion or is it filtered out due to the mapping quality? Can anyone suggest an alternative tool / setting for filtering the pileup? Thanks, Laura Laura Reinholdt, PhD Research Scientist Genetic Resource Sciences The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609-1500 (207) 288-6000, ext. 6693

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Re: [galaxy-user] Pilup file and counting reads in 200bp windows
by Jennifer Jackson 04 Oct '11

04 Oct '11

Hello Di, Once the data is in pile-up format, the read identifier is lost, so summarizing per-read over a range is not possible. However, you could graph the data, which would graph the number of reads represented per reference genome position. Do this with "Graph/Display Data -> Histogram", on the pileup coverage value and setting the number of breaks per chromosome so that they end up being each ~200 bases. Or, going back to the BAM/SAM data, the tool "Regional Variation -> Make windows" can create 200 bp windows per chromosome (given an input BED3 file - chrom, start, end). Then use this and the BAM/SAM alignments (converted to interval) as input for the tool "Regional Variation -> Feature coverage". Hopefully one of the options will work for you, Best, Jen Galaxy team ps. Please send all questions directly to the mailing lists unless they contain private data/links. On 10/4/11 3:18 PM, Di Nguyen wrote: > Hi Jennifer, > > I have some Chip seq data that I can map with bwa, then I can generate a > pileup file. My question is how do we count how many reads in a 200bp > windows, say for Chromosome X or autosomes? Please help! > > My utmost appreciation, > > Di Nguyen > UWashington > > > -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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SamTools processing issue
by Golbus, Jessica 04 Oct '11

04 Oct '11

Hi- I am currently working with one of Illumina's older Bam files and trying to run SamTools Pileup. Unfortunately, the server has repeatedly timed out on me and I am unable to run the program on my file. I was wondering if other people are having trouble running Samtools on human genome .bam files or whether this is secondary to the way the file is configured (i.e. it was first run through Illumina's proprietary software and provided as a .bam without an accompanying fastq file)? Thanks for your help! Jessie ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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SNPEff 2.0.2 Wrapper Problem / Partial Fix
by John David Osborne 03 Oct '11

03 Oct '11

Hi Pablo, We recently installed 2.0.2 SnpEff at the UAB Galaxy instance (thanks for adding those mycoplasma genomes to SNPEff!) but we ran into some problems with the galaxy wrapper. It looks like it is for an older version of SnpEff and it chocks on the input options it is fed. I replaced the input format section in snpEff.xml with: <param name="inputFormat" type="select" label="Input format"> <option value=" -i txt ">Text</option> <option value=" -i pileup ">Pileup</option> <option value=" -i vcf ">VCF 4</option> <option value=" -i bed ">BED</option> </param> It runs now, although I am sure there are other additional fixes that could be made to update the wrapper. Right now there is no option in the galaxy wrapper to output to VCF. If you could fix this that would be great, otherwise I can look into the format of the galaxy wrapper xml – something I need to do at eventually anyway. -John

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upload zip file to custom tool
by Brent Pedersen 03 Oct '11

03 Oct '11

Hi, I have followed the wiki and built a custom tool on a local galaxy installation. One of the inputs is a zip file. It seems galaxy automatically unpacks it and keeps only the first file. Is there any way I can tell galaxy not to unzip the file? I tried to register .zip as a datatype, but that didn't seem to change the behavior. thanks for any help. $tool.xml is below in case it helps. -Brent <command interpreter="python">charmqc.py $xyszip $output $organism</command> <inputs> <param format="xys.zip" name="xyszip" type="data" label="Zip of .xys files"/> <param type="select" name="organism" label="organism"> <option value="Human">Human (hg18)</option> <option value="Mouse">Mouse (mm8)</option> </param> </inputs> <outputs> <data format="data" name="output" /> </outputs>

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sequence analysis full tutorial
by frederic lepretre 30 Sep '11

30 Sep '11

hi, I'm a little bit rooky in using galaxy, and ask if someone could send me a tutorial. precisely, I'm using ion torrent data that I succeed to load. but what to do after? thanks a lot fred -- ********************************************************* * Dr Frédéric Leprêtre * * Institut pour la Recherche sur le Cancer de Lille * * Plateforme de génomique fonctionnelle * * Agilent - Affymetrix - SoliD3 * * Place de Verdun 59045 Lille cedex * * * * tel. 03 20 16 92 20 poste 2339 * * fax. 03 20 16 92 29 * * http://www.ircl.org/ * * frederic.lepretre(a)inserm.fr * * ou * * frederic.lepretre(a)univ-lille2.fr * *********************************************************

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non-coding RNA
by dongdong zhaoweiming 30 Sep '11

30 Sep '11

Hi, I want to evaluate wherther my assembly transcripts produced by trinity is protein-coding or notcoding. I found two methods which are "txCdsPredict" program from the UCSC(John R Prensner,2011) and Codon Substitution Frequencies,CSF(Michael F. Lin,2008). I wonder if galaxy can do this? Thanks a lot! weimin zhao

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Fwd: de novo assembly
by John Nash 29 Sep '11

29 Sep '11

Forgive the forwarded email. Not used to working from an iPad. > On 2011-09-29, at 7:58 PM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote: > >> On Thu, Sep 29, 2011 at 7:49 PM, Cecilia Tamborindeguy >> <ctamborindeguy(a)ag.tamu.edu> wrote: >>> Hello, >>> >>> I would like to know if Galaxy can do de novo assembly without a reference >>> genome. >>> >>> Thanks. >>> >>> Cecilia >> >> Are you trying to use the Public Galaxy or a local install? There >> are several assemblers with Galaxy Wrappers on the Galaxy >> ToolShed (e.g. Roche "Newbler", and MIRA 3) which you could >> add to your own local Galaxy if you have one. >> >> However, do novo genome assembly can be very computationally >> demanding, so not many Galaxy Instances will want to offer it. >> >> Peter > > I would like to echo Peter's advice. (Again, that's twice in 5 min from 2 different lists. I promise you I'm not stalking you, Peter). > > Genome assembly is a bit of a dedicated domain with respect to expertise and time. If possible, if you are assembling a lot of genome data, you really should set yourself up properly with a multiple-CPU unix box with a lot of RAM and dedicate it to assembly. Install MIRA, Newbler, Velvet, AMOS, samtools, bamtools, bedtools, Staden, phred/phrap/consed on it, and you can assemble and interconvert data to your heart's content. > > Galaxy is a wonderful and useful service but assembling genomes does require dedicated power and expertise, and preferably in house. I just forked out for a 64 CPU processor with 1 TB RAM bc we assemble lots of genomes. You don't have to go that far but a 3-4 quad processor box with 128 GB RAM and 1 TB disk should be on your mind. > > John

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