SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Soap Output File Error: Can't write rahul.m.dhodapkar Bioinformatics 11 07-06-2015 06:34 AM
tophat + cufflinks: strand information Zimbobo Bioinformatics 29 04-20-2012 01:35 AM
GATK: unable to write data to BAM schedule file bjchen Bioinformatics 5 02-13-2012 01:21 AM
adding platform information to a bam file efoss Bioinformatics 2 09-12-2011 11:22 AM
Bowtie, BWA, strand information Zimbobo Bioinformatics 6 04-24-2010 09:30 AM

Reply
 
Thread Tools
Old 11-04-2011, 08:01 AM   #1
droog_22
Member
 
Location: Vienna

Join Date: Nov 2010
Posts: 10
Default Re-write strand information in BAM file

Hello,

I have a quick and simple questions: Is there a ready-to-use tool which allows me to re-write the strand information in a BAM file, such that reads which mapped on the forward strand are stored as mapping to the reverse strand and vice-versa?

I know how to do it with samtools and awk, but I was wondering if there was a faster solution without going through an intermediate SAM file.

Cheers, Daniel
droog_22 is offline   Reply With Quote
Old 11-07-2011, 04:25 AM   #2
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

I'm not quite sure what you are trying to do (or why), but in principle if you can program in Java you should be able to do this via Picard, or using the samtools C API, perhaps via Python (pysam) or a similar language specific wrapper.
maubp is offline   Reply With Quote
Reply

Tags
bam, strand information

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 11:21 PM.


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