SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to fetch sequence from chromosome coordinates kumardeep Bioinformatics 6 05-29-2015 01:40 AM
Galaxy Fetch Sequence for negative Strand Fernas Bioinformatics 0 12-22-2013 11:10 AM
Ensembl database fetch sequence problem roger770507 Bioinformatics 2 12-02-2013 01:56 AM
fetch transcripts assembled by cufflinks asling Bioinformatics 6 09-27-2012 09:46 PM
how to fetch the snp allele frequency? dzmtnvmt Bioinformatics 3 06-21-2011 03:44 AM

Reply
 
Thread Tools
Old 03-13-2017, 02:28 AM   #1
pkseq2017
Junior Member
 
Location: Germany

Join Date: Mar 2017
Posts: 6
Default pysam.fetch and gene_id

Hi there,

Does anyone know if/how pysam.fetch would accept gene_ids instead of ref+coordinate?


Thanks a lot for your help
pkseq2017 is offline   Reply With Quote
Old 03-13-2017, 02:45 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

It won't accept that at all. You will need to convert that to a genomic range.
dpryan is offline   Reply With Quote
Old 03-13-2017, 03:02 AM   #3
pkseq2017
Junior Member
 
Location: Germany

Join Date: Mar 2017
Posts: 6
Default

Good to know, thank you!

So basically would be an extra layer of translating from some ref file to coordinates I guess?
pkseq2017 is offline   Reply With Quote
Old 03-13-2017, 03:07 AM   #4
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

Exactly, you'd need to store the gene_id to position association somewhere.
dpryan is offline   Reply With Quote
Old 03-13-2017, 05:04 AM   #5
pkseq2017
Junior Member
 
Location: Germany

Join Date: Mar 2017
Posts: 6
Default

Alright! Thanks for your help
pkseq2017 is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 06:38 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO