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

[Anonymous Monk]

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

[pmqs]

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.