Determine unique mapped reads

[Hongxiang2023]

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!!

[guoweilong]

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!! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Hongxiang2023]

Thank you! But what are the criteria used to determine the unique best hit?

[guoweilong]

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? — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>