bedtools multicov not running
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
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ariel.balter
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Bnf83
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Bnf83
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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!
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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.
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.
what bedtools version you are using?
I'm using bedtools v2.16.1