Good afternoon, I'm working with target capture sequencing and I would like to know the coverage of my target genes, which I just have in fasta format. I already have my reads aligned into the genome and in bam format and I also already did the SNP calling (with freebayes). So my questions are: - How can I calculate the coverage of my target genes in the bam files I have? - Could be a way to just do the SNP calling of those genes?
I'm aware that with bedtools I could calculate the coverage, but is asking me a bed file that I don't have.
Any type of help will be apreciate it, thanks!
1 answer
What genome are you working with ? For any genome, if you already have genes in fasta, there must be genomic coordinates for those genes in either GTF/GFF or bed format. If you have GTF, convert it to a bed file of exons or gene start end and then calculate coverage using bedtools. Either you can calculate per base pair or per region ( for each gene)
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merge paired-end sequencing
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genome coverage visualization
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quality check of bam files
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Phasing with Beagle
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I'm working with the genome of Podarcis muralis, a lizard species. I'm going to check right now if I can find the bed file, thanks!
But how can I obtain the genomic coordinates?
You can find the genomic coordinates in the GFF file on the genome page for Podarcis here. Look for genome annotation in GFF or tabular format in the box at top of the page.