Open Hongxiang2023 opened 2 years ago
All output reads in BAM files generated by BS-Seeker2 are reads with unique best hit.
Weilong
At 2022-05-12 14:44:14, "Hongxiang Fu" @.***> wrote:
Hi,
I'm just curious how the unique mapped reads are counted? Is it using the mapping quality threshold or XA and SA tag to filter out the reads? Thank you!!
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Thank you! But what are the criteria used to determine the unique best hit?
From the bam files generated by bowtie/bowtie2, we can extractet the count of mismatched nucleotides (for end-to-end) and the alignment score (for local alignment). Then the top best two reads for each instance were compared to deternine the unique best hit.
Best, Weilong
At 2022-05-13 13:50:32, "Hongxiang Fu" @.***> wrote:
Thank you! But what are the criteria used to determine the unique best hit?
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Hi,
I'm just curious how the unique mapped reads are counted? Is it using the mapping quality threshold or XA and SA tag to filter out the reads? Thank you!!