Microbial gene coverage from blast result

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4 months ago

aanchal.yadav • 0

Hello all I am new to BLAST and Biostars. I have removed human-mapped reads from RNA-Seq data and did Kraken2 and Bracken analysis using the microbial reads. Using the Kraken Tool, I retrieved the microbial reads. Then I performed BLASTx in order to find the microbial genes present in the data. Now, the main question is to find the coverage of those genes. I used the following formula : (query start - query end)/total gene length in nucleotides [from Uniprot] multiply by 100. But I am getting the coverage more than 100% also for a few genes. Is the formula correct? Or please suggest some tool or formula or code to calculate the gene coverage using BLAST result.

Thank You

gene coverage • 304 views

ADD COMMENT • link 4 months ago by aanchal.yadav • 0

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What is qcovhsp (high scoring segment pair) in BLAST output. Can we use this parameter to calculate the gene coverage?

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