Question: Parsing genomeCoverageBed (-bga flag) result to see multiple contigs coverage!
gravatar for marcela.uliano
3.3 years ago by
European Union
marcela.uliano60 wrote:

Hey guys!

I'm trying to calculate one thing and I'm sure someone else has also done this. So maybe someone have a script ready!

I have a draft de novo genome, and augustus predicted too many genes (54 thousand), so I've aligned my RNA-seq to the exons predicted to discharge the exons with bad (5 or less) bases covered by rna-seq reads.

So, I have submitted my bam.sorted file to genomeCoverageBed script with the flag -bga, so I can have the info of 0 coverage.

My output is like this:

itr6_2569_pilon_pilon_pilon_pi.g4.t1.cds1 0 62 0

itr6_2569_pilon_pilon_pilon_pi.g4.t1.cds1 89 90 0

itr6_2569_pilon_pilon_pilon_pi.g4.t1.cds1 224 225 0

itr6_2569_pilon_pilon_pilon_pi.g4.t1.cds1 252 253 0

Which means, for example for line 1, the exon 'tr6_2569_pilon_pilon_pilon_pi.g4.t1.cds1' has zero coverage in the interval 0 to 62 bases. Next line shows another interval for the same exon...

I also have a file with the exon IDs and their total length. Like this:

tr6_2575_pilon_pilon_pilon_pi.g61.t1.cds5 105

itr6_2575_pilon_pilon_pilon_pi.g61.t1.cds6 69

itr6_2575_pilon_pilon_pilon_pi.g61.t1.cds7 114

itr6_2575_pilon_pilon_pilon_pi.g61.t1.cds8 90

So, the info I would like to extract is: to select the exons that have 70% or more of its total sequence covered by 0 bases.. So I can take them out of my genome prediction.

Does anyone has done that and can help me?

Thank you so much!

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by marcela.uliano60

Have you considered just using the TransRate package?

ADD REPLYlink written 3.3 years ago by Devon Ryan93k

Thanks, Devon! I'll have a look!

I was also thinking in a simple solution: maybe just using 'samtools indxstat' with my bam file. I wont have information of coverage per base, but I'll have size of contig and number of reads mapped, so a raw estimate I can do from there.

I'll play around with different things today.. Thanks!

ADD REPLYlink written 3.3 years ago by marcela.uliano60
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