Wednesday 2 May 2012

BED file format ...


[$bash] coverageBed -a xc.bed -b xb.bed
Unexpected file format.  Please use tab-delimited BED, GFF, or VCF. Perhaps you have non-integer starts or ends at line 1?


Can't believe I wasted 2 hours trying all options to debug the above ... ONLY to suddenly remember that my colleague probably passed me the xb.bed which she generated in Windows ...

I was witch hunting for double tabs, chr names  ... etc  when

dos2unix xb.bed 

solved it in 5 secs ... :/

3 comments:

  1. I wonder how many hour are wasted every year with debugging different line endings! I know I've wasted my fair share!

    ReplyDelete
  2. Thank you, wasted two hours on the exact same problem, decided to google it. Helped a lot. BR

    ReplyDelete
  3. hi all,

    I seem to have some difficulties solving this bug. I have this file:
    5262147 5262433 334
    85626381 85656805 30472
    54522461 54522626 213
    30281944 30282086 190

    but when i run it in intersect i get this error also (Unexpected file format. Please use tab-delimited BED, GFF, or VCF. Perhaps you have non-integer starts or ends at line 1?)

    when i run this: cat -e i.bed | more
    i get this:
    5262147 5262433 334 $
    85626381 85656805 30472 $
    54522461 54522626 213 $
    30281944 30282086 190 $

    someone have any advice?

    Thanks

    ReplyDelete

Datanami, Woe be me