Calculate distribution of reads over the reference genome

Question

[pixie@bioinfo]

Hello, is there a tool which I could use to calculate the distribution of reads over the reference genome ? I have a visual representation of two different wetlab protocols, one giving a sligtly better distribution than the other menthod and would like to represent it quantitively. I have bam and bigwig files for the data and fasta file for the reference genome.

[Pierre Lindenbaum]

mosdepth ?

[Joe]

Perhaps a bit dated now, but are you not just looking for something like Qualimap: http://qualimap.conesalab.org/ ?

It will give you a graphical representation of your coverage depth and other stats etc

Answer 1

[Istvan Albert]

For RNA-Seq the concept of transcript integrity can be used to characterize the evenness of the coverage over the entire transcript.

• Measure transcript integrity using RNA-seq data BMC Bioinformatics, 2016

the same concept would also apply to any other sequencing protocol, in that case you would need to figure out what intervals to measure it over.