Question: Bus Error When Using Bedtools Coverage
gravatar for R
6 weeks ago by
R0 wrote:


I am new to bioinformatics, and this forum, so apologies if I have done anything incorrectly, or if this is a stupid question. But I have attempted to search for the answer and not gotten anything relevant to what I'm doing. Currently I am trying to use bedtools coverage with my windows (.bed file) and data (.bam file), however, each time I try to run it, I get 'bus error,' and the job will not complete. Does anyone know what this means, and how I can fix it? All help is appreciated!

ADD COMMENTlink written 6 weeks ago by R0

Here's an alternative that performs the same calculation: A: Use bedtools intersect to see how much coverage you had of a specific coordinate

ADD REPLYlink written 6 weeks ago by Alex Reynolds31k

Thank you for your help! But I even get the 'bus error' as I'm trying to sort the .bed file.

ADD REPLYlink written 6 weeks ago by R0

Perhaps post your files somewhere (Google Drive etc.) and copy/paste your command. That would help troubleshoot the exact error message.

ADD REPLYlink written 6 weeks ago by Alex Reynolds31k
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