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BSSeeker / BSseeker2

A versatile aligning pipeline for bisulfite sequencing data
http://pellegrini.mcdb.ucla.edu/BS_Seeker2/
MIT License
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[HELP] Unique mapped reads ratio #45

Open hmyh1202 opened 2 years ago

hmyh1202 commented 2 years ago

Hello, WeiLong:

In your BSSeeker2 Paper, how to caculate  the mapping ratio of different software? 
Some software could  report the alignment ratio od unique. The BSMAP report the high quality aligned reads of mapq 30, while the bismark report unique reads but not filter out the mapq 30 align reads.

So how to get the unique reads of each software for comparision.

Thank you !

guoweilong commented 2 years ago

I may not follow your question.

Why directly counting the mappable reads in the output bam files would not solve the problem?

Weilong

At 2022-04-19 14:36:51, "Grace Bisulfite" @.***> wrote:

Hello, WeiLong:

In your BSSeeker2 Paper, how to caculate the mapping ratio of different software? Some software could report the alignment ratio od unique. The BSMAP report the high quality aligned reads of mapq 30, while the bismark report unique reads but not filter out the mapq 30 align reads.

So how to get the unique reads of each software for comparision.

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: @.***>

hmyh1202 commented 2 years ago

For BSMAP only report unique mapped read pairs which mapq is 30, while the bismark report unique read pairs that did not filter mapq value. If filter low mapq mapped reads of bismark，the final number of reads pairs would differ a lot.  I think it not in identical on-line for comparison when directly counting the mappable reads in the output bam.

------------------ 原始邮件 ------------------ 发件人: "BSSeeker/BSseeker2" @.>; 发送时间: 2022年4月19日 3:53PM @.>; @.**@.>; 主题: Re: [BSSeeker/BSseeker2] [HELP] Unique mapped reads ratio (Issue #45)

I may not follow your question.

Why directly counting the mappable reads in the output bam files would not solve the problem?

Weilong

At 2022-04-19 14:36:51, "Grace Bisulfite" @.***> wrote:

Hello, WeiLong:

In your BSSeeker2 Paper, how to caculate the mapping ratio of different software? Some software could report the alignment ratio od unique. The BSMAP report the high quality aligned reads of mapq 30, while the bismark report unique reads but not filter out the mapq 30 align reads.

So how to get the unique reads of each software for comparision.

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