Re^4: (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

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Re^5: (OT) help reading a bgzip file by pmqs (Friar) 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` [download] 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.	[reply] [d/l]