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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)

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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...

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

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Last updated: Jan 29 '16