Beefy Boxes and Bandwidth Generously Provided by pair Networks
good chemistry is complicated,
and a little bit messy -LW
 
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.


Comment on Re^5: (OT) help reading a bgzip file
Download Code

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 examining the Monastery: (17)
As of 2015-07-06 13:49 GMT
Sections?
Information?
Find Nodes?
Leftovers?
    Voting Booth?

    The top three priorities of my open tasks are (in descending order of likelihood to be worked on) ...









    Results (75 votes), past polls