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Re^5: (OT) help reading a bgzip file

by pmqs (Pilgrim)
on May 04, 2011 at 10:49 UTC ( #902846=note: print w/replies, xml ) Need Help??


in reply to Re^4: (OT) help reading a bgzip file
in thread (OT) help reading a bgzip file

If file is really just a gzip file then try checking that it isn't corrupt
gunzip -tv file.bgzip
Looking at http://samtools.sourceforge.net/SAM1.pdf (which I think is the reference for the file format used by bgzip) it looks like the payload data (BAM) in the bgzip file is not ascii text - that would explain why you are seeing non-ascii text when you run it through zless.

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