gravatar for Happy_flower

2 hours ago by

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!



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