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BSSeeker / BSseeker2

A versatile aligning pipeline for bisulfite sequencing data
http://pellegrini.mcdb.ucla.edu/BS_Seeker2/
MIT License
60 stars 25 forks source link

Determine unique mapped reads #47

Open Hongxiang2023 opened 2 years ago

Hongxiang2023 commented 2 years ago

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 commented 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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Hongxiang2023 commented 2 years ago

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

guoweilong commented 2 years ago

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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