[$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 ... :/
I wonder how many hour are wasted every year with debugging different line endings! I know I've wasted my fair share!
ReplyDeleteThank you, wasted two hours on the exact same problem, decided to google it. Helped a lot. BR
ReplyDeletehi all,
ReplyDeleteI 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