-----Original Message----- From: galaxy-user-bounces@lists.bx.psu.edu [mailto:galaxy-user-bounces@lists.bx.psu.edu] On Behalf Of galaxy-user-request@lists.bx.psu.edu Sent: Tuesday, June 14, 2011 9:00 AM To: galaxy-user@lists.bx.psu.edu Subject: galaxy-user Digest, Vol 60, Issue 14 Send galaxy-user mailing list submissions to galaxy-user@lists.bx.psu.edu To subscribe or unsubscribe via the World Wide Web, visit http://lists.bx.psu.edu/listinfo/galaxy-user or, via email, send a message with subject or body 'help' to galaxy-user-request@lists.bx.psu.edu You can reach the person managing the list at galaxy-user-owner@lists.bx.psu.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of galaxy-user digest..." HEY! This is important! If you reply to a thread in a digest, please 1. Change the subject of your response from "Galaxy-user Digest Vol ..." to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Why? 1. This will keep the subject meaningful. People will have some idea from the subject line if they should read it or not. 2. Not doing this greatly increases the number of emails that match search queries, but that aren't actually informative. Today's Topics: 1. SAM to bigbed (Aleks Schein) 2. Re: SAM to bigbed (Jennifer Jackson) 3. GenBank Submission - How to Generate Fasta (not fastq) files (John David Osborne) ---------------------------------------------------------------------- Message: 1 Date: Mon, 13 Jun 2011 18:42:45 +0200 From: Aleks Schein <aleks@mb.au.dk> To: galaxy-user@lists.bx.psu.edu Subject: [galaxy-user] SAM to bigbed Message-ID: <20110613184245.14175jqs5ml9mqrp@webmail.nfit.au.dk> Content-Type: text/plain; charset=ISO-8859-1; DelSp="Yes"; format="flowed" Hi, Is it possible to generate a bigbed or bigwig file from SAM (or BAM) file using Galaxy? It looks like there is such option in the full version of SAMTools, but I have no appropriate machine to run SAMTools. Thanks, Aleks ------------------------------ Message: 2 Date: Mon, 13 Jun 2011 10:03:04 -0700 From: Jennifer Jackson <jen@bx.psu.edu> To: Aleks Schein <aleks@mb.au.dk> Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] SAM to bigbed Message-ID: <4DF642C8.3070000@bx.psu.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Aleks, There is no function in Galaxy for this in one step, but there are other options: 1) only convert to BAM and view at UCSC that way, if visualization is your goal. This preserves the primary sequence information in the file so that it can be viewed/used in downstream analysis. 2) use "Generate Pileup" then "Pileup-to-Interval". Interval can be changed to BED using the pencil icon (you may need to arrange column order first to meet spec, as BED columns must be in a specific order, as defined on any of the tools involving BED files). The resulting BED file can then be condensed by "BED-to-bigBed". This loses the primary sequence information - only coordinates are retained - may or may not be desirable. Hopefully this helps, Jen Galaxy team On 6/13/11 9:42 AM, Aleks Schein wrote:

Hi, Is it possible to generate a bigbed or bigwig file from SAM (or BAM) file using Galaxy? It looks like there is such option in the full version of SAMTools, but I have no appropriate machine to run SAMTools.

Thanks,

Aleks ___________________________________________________________ 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:

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-- Jennifer Jackson http://usegalaxy.org/ http://galaxyproject.org/ ------------------------------ Message: 3 Date: Mon, 13 Jun 2011 13:34:11 -0500 From: John David Osborne <ozborn@uab.edu> To: "galaxy-user@bx.psu.edu" <galaxy-user@bx.psu.edu> Subject: [galaxy-user] GenBank Submission - How to Generate Fasta (not fastq) files Message-ID: <27F664987FEADB4EA29031F58BC42B3E02144922@UABEXMBS5.ad.uab.edu> Content-Type: text/plain; charset="iso-8859-1" I still haven't found an easy solution to this problem and I am afraid I'm going to have to write one my own - which makes little sense as I bet this has been solved thousands of times! Can anybody point me to a script/software to convert a samtools pileup file into a fasta consensus file? It would be nice to set coverage thresholds, etc... but I'll take anything I can work with. The best google could do for me was this: http://biostar.stackexchange.com/questions/1389/how-to-generate-a-consen sus-fasta-sequence-from-sam-tools-pileup Not that helpful, -John P.S. If there is a better way of doing this (something other than samtools) I'm all ears.