X chromosome in bedtoolsIntersect

Question

[wiscoyogi]

I wanted to get the intersection from a set of bam files that I have and a bed file that I made of some genes that I'm interested in. I made the bedfile using gtf2bed with no error messages.

when I use bedtools intersect -a sample.bam -b reference.bed between a bam file and the bed file of the genes I'm interested in, I keep getting the error:

***** ERROR: illegal character 'X' found in integer conversion of string "X". Exiting...

I greped the bed file and it looks like they're coming from the X chromosome...

Including a subset of the bed file here:

479:MTMR1   X   150692971   150765103   +   gene
480:FAM58A  X   153587919   153600045   -   gene
481:RENBP   X   153935263   153944691   -   gene
482:RPL10   X   154389955   154409168   +   gene

I don't get this error (e.g. the command runs) if I run with bedtools intersect -a sample.bam -b reference.gtf but the outputted file is gibberish.

I'm not sure what to do here because these are genes on the X chromosome and I've seen nothing like this in the cases online.

Would be grateful for any/all suggestions here.

[Pierre Lindenbaum]

Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. If an answer was not really helpful or did not work, provide detailed feedback so others know not to use that answer.

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Answer 1

[Pierre Lindenbaum]

That's NOT a bed file.

A bed file is chrom/start/end and your file is name/chrom/start/end