Can GenomeBrowse read BS-seq BAM files produced by Bismark?
When I try I get error "BAM file is out of order at line 6 (error code 3)". (GB 2.1.0)
When I try I get error "BAM file is out of order at line 6 (error code 3)". (GB 2.1.0)
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...
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.
Asked: 2016-01-28 15:34:31 -0600
Seen: 7,747 times
Last updated: Jan 29 '16
