Beefy Boxes and Bandwidth Generously Provided by pair Networks
Clear questions and runnable code
get the best and fastest answer

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

Replies are listed 'Best First'.
Re^5: (OT) help reading a bgzip file
by pmqs (Monk) 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 (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.

Log In?

What's my password?
Create A New User
Node Status?
node history
Node Type: note [id://902745]
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others surveying the Monastery: (7)
As of 2016-10-21 12:23 GMT
Find Nodes?
    Voting Booth?
    How many different varieties (color, size, etc) of socks do you have in your sock drawer?

    Results (289 votes). Check out past polls.