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Re^4: (OT) help reading a bgzip file

by Anonymous Monk
on May 03, 2011 at 16:04 UTC ( #902745=note: print w/ replies, xml ) Need Help??


in reply to Re^3: (OT) help reading a bgzip file
in thread (OT) help reading a bgzip file

hi. it says what i put in the last post - that it is a gzip compressed data with extra field but when i read it with zless it is nonsense and contains mostly this string ^@ intermixed with ascii characters


Comment on Re^4: (OT) help reading a bgzip file
Re^5: (OT) help reading a bgzip file
by pmqs (Scribe) on May 04, 2011 at 10:49 UTC
    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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