Ask Your Question
0

Can GenomeBrowse read BS-seq BAM files produced by Bismark?

asked 2016-01-28 15:34:31 -0600

Kim Taylor gravatar image

updated 2016-01-28 15:40:04 -0600

When I try I get error "BAM file is out of order at line 6 (error code 3)". (GB 2.1.0)

edit retag flag offensive close merge delete

1 answer

Sort by ยป oldest newest most voted
0

answered 2016-01-29 14:57:37 -0600

Hi Kim,

Unfortunately GenomeBrowse can only visualize sorted BAM files. Since your files are not sorted you will not be able to use GenomeBrowse until you can get the files sorted in genomic order.

There are several options for sorting your files including SAMTools, which is a free command line program for working with SAM/BAM files.

Let me know if you have any further questions.

Thanks, Jami...

edit flag offensive delete link more
Login/Signup to Answer

Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.

Question Tools

Follow
1 follower

Stats

Asked: 2016-01-28 15:34:31 -0600

Seen: 5,556 times

Last updated: Jan 29 '16