Is it okay to convert bam files to fastq and then getting seqkit results?
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9 weeks ago
Baran • 0

I'm sorry if this is a non-sense question but I am a rookie and although I searched about this I couldn't find any decent answer. I had the fastq files but they somehow became corrupted. I need to get Q20 Q30 scores for the fastq file but I only have bam files right now. So, I wonder if it is okay to get fastq files by converting bam files with the gatk SamToFastq convert function and then getting the Seqkit stat results?

bam fastq QC seqkit • 204 views
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Entering edit mode
9 weeks ago
Chris Dean ▴ 220

That sounds reasonable to me ;)! Quality scores are preserved when converting from BAM to FASTQ.

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