Beefy Boxes and Bandwidth Generously Provided by pair Networks
laziness, impatience, and hubris
 
PerlMonks  

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

by pmqs (Monk)
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.

Log In?
Username:
Password:

What's my password?
Create A New User
Node Status?
node history
Node Type: note [id://902846]
help
Chatterbox?
and the web crawler heard nothing...

How do I use this? | Other CB clients
Other Users?
Others having an uproarious good time at the Monastery: (5)
As of 2016-07-25 12:09 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?
    What is your favorite alternate name for a (specific) keyboard key?


















    Results (224 votes). Check out past polls.