bedtools multicov not running

Question

[Bnf83]

Hi guys, I'm trying to count the number of reads per gene (RNA Seq analysis) to perform the gene expression analysis. I'm using: bedtools multicov -bams my_file.bam -bed Human_genes.bed > gene_counts.txt Strangely, the gene_counts.txt file is exactly equal to the Human_genes.bed file. Since no Error or Warning message is generated I don't know how to deal with this issue. Does anyone have experience of this kind of error?

Thanks in advance

[hns]

Because you are giving it a bed file, it will tell you how many regions from that bed file are in the bam file and it seems like you have all of them.

[Bnf83]

Yes, you' re right, but as from here: http://bedtools.readthedocs.org/en/latest/content/tools/multicov.html I expect the count of alignments but this does not appear in the output file.

[Varun Gupta]

what bedtools version you are using?

[Bnf83]

I'm using bedtools v2.16.1

Answer 1

[ariel.balter]

I'm having the same issue. Is it a problem with the format of the input files? If you figure it out, post the answer!