Calculate gene coverage from Blast results

Question

[Happy_flower]

Hi all

Does anyone have an idea how I can calculate the number of mapped reads, unmapped reads, and the gene coverage from local BLAST results. The -outfmt 6 option gives me a tabular output that contains alignment length (sequence overlap), start of alignment in query, end of alignment in query, start of alignment in subject, and end of alignment in subject. As genome coverage= number of reads + read length/ length of gene, I wondered whether I can utilize these output values to determine coverage of target genes. I am new to BLAST, so I will be grateful if you have any suggestions.

Thanks!

[gb]

Are you following a specific method from a paper or something? As far as I know your question is a bit unusual. Normally terms like mapped reads, unmapped reads, and the gene coverage has to with mapping of reads and not blasting.

Mapping of reads can be done with programs like bowtie, BWA, minimap2. BLAST is a program to search DNA sequences in a database.

Answer 1

[Istvan Albert]

What you could do it convert your tabular Blast file to a BED file, which usually means just cutting a few columns out, then run

 bedtools coverage

or

bedtools genomecov