How to find coverage for RNA-seq, solid data?

[pinki999]

Hi,

I am trying to look into the coverage of transcriptome (solid) data but no luck. I downloaded the reference bed file from UCSC genome browser for the know genes and used bedtools to find the coverage. I am getting negative percentage. Anyone out there with a solution for this?

Thank you

[shurjo]

Hi,

I am trying to look into the coverage of transcriptome (solid) data but no luck. I downloaded the reference bed file from UCSC genome browser for the know genes and used bedtools to find the coverage. I am getting negative percentage. Anyone out there with a solution for this?

Thank you

I've used coevrageBed from BedTools for this and negative percentages sounds somewhat surprising. Can you post the syntax you used on the command line and maybe a short section from your output file?

[pinki999]

Hi,

I used the following command

coverageBed -hist -s -abam input.bam -b known_genes.bed

and in the attachment you can find the short output file.

Thank you.