Question: The Original Subject For The Thread
gravatar for David Wang
6.6 years ago by
David Wang10
David Wang10 wrote:
[] On Behalf Of To: Subject: galaxy-user Digest, Vol 60, Issue 14 Send galaxy-user mailing list submissions to To subscribe or unsubscribe via the World Wide Web, visit or, via email, send a message with subject or body 'help' to You can reach the person managing the list at 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 To: Subject: [galaxy-user] SAM to bigbed Message-ID: <> 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 To: Aleks Schein <> Cc: Subject: Re: [galaxy-user] SAM to bigbed Message-ID: <> 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 SAMTools. -- Jennifer Jackson Message: 3 Date: Mon, 13 Jun 2011 13:34:11 -0500 To: "" <> Subject: [galaxy-user] GenBank Submission - How to Generate Fasta (not fastq) files Message-ID: <> 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: 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. URL: <http:"" pipermail="" galaxy-="" user="" attachments="" 20110613="" f579="" 0e82="" attachment-0001.html=""> _______________________________________________ galaxy-user mailing list End of galaxy-user Digest, Vol 60, Issue 14 ******************************************* The preceding email message and any attachments may be confidential. If you have received this message in error, please (i) do not read it or if you have already read it, disregard it, (ii) reply to the sender that you received the message in error, and (iii) erase or destroy the message and its attachments. Any unauthorized use or distribution of this message or its attachments is prohibited. Thank you.
samtools bam • 1.0k views
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