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jianhong / ATACseqQC

ATAC-seq Quality Control
https://jianhong.github.io/ATACseqQC/articles/ATACseqQC.html
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Question about the read filtering by bamQC #45

Open etiennedanis opened 3 years ago

etiennedanis commented 3 years ago

Hi Jianhong,

Besides the reads with low alignment scores, the reads derived from mitochondrial DNA and the PCR/optical duplicates, are there any other filters applied by bamQC? What are the parameters used for removing the reads with low alignment scores? Is it only reads with a MAPQ score (as in samtools view -q 30) below 30 (based on bowtie2 alignment) being removed? Are any other reads being removed?

Thank you so much in advance! Best, Etienne

jianhong commented 2 years ago

You may want to check the documentation of ?readBamFile about the flag section.