Calculating Read/Coverage Depth per Base Pair from a GFF3 File

[dgosting]

Hey, this is my first post and have been searching for hours trying to find a clear answer to this but could not for the life of me. Any input would be much appreciated. Thanks!

I was wondering if it is possible to calculate read/coverage depth per base pair using just a GFF3 file. Basically is there a script that you can plug in just a .gff3 and it will calculate and graph coverage depth of each base pair across the entire genome?

And if it is possible, where/what exactly would I look for in the gff3 file to do this?

[GenoMax]

Take a look at coverageBed: http://bedtools.readthedocs.org/en/l.../coverage.html

I assume you have your data available as aligned BAM files.

[dgosting]

Hey, thanks for feedback. Yes I do have a BAM file and have looked at tools/programs like bedtools. But is it possible to calculate the read/coverage depth using just the .gff3 file format or must I have an additional file like the bam to do this?

[GenoMax]

The GFF file is only providing mileposts as to where you features of interest are located in the genome. You are using that interval information to get the read/coverage depth from your aligned sequence data that is contained in the BAM file. So minimally you need bedtools, GFF/bed file of features of interest and the aligned sequence data in sorted BAM file format.