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Write down read qual from the `fastq` input into the `sam` output file? #32

Closed y9c closed 1 year ago

y9c commented 3 years ago

Seem that read quality field is missing in the sam output file.

boratyng commented 3 years ago

Magic-BLAST does not use read quality scores, because they are not always accurate. The scores are not included in the SAM report.

@yech1990, are quality scores needed in downstream analysis?

y9c commented 3 years ago

Hi @boratyng

Yes. I know BLAST do not use quality score during the mapping step. But to make them output sam file compatible with other NGS tools, I think Magic-BLAST can append the quality score back into the sam file after the mapping.

boratyng commented 3 years ago

Yes, we can do this, will try for the next release.

boratyng commented 1 year ago

Hi @y9c, Magic-BLAST 1.7.0 which was recently released reports read quality scores in the SAM output. Here are installation instructions: https://ncbi.github.io/magicblast/doc/download.html.