CGMap file the count of reads showing C or T here does not make scense

[salehsereshki]

Hi,

I wanted to work with the output of call_methylation command, CGMap file. In this file, at the last column, the reported number is "the count of reads showing C or T here". I calculated the read coverage for my data, and it is about 80, but the mean of the last column of this table is only 1.5. Do you know why is that? The Mappability is reported 34.7435%.

[freyayang]

Hi, I have the same issue with you. Do you figure out what's the problem? Thank you!

[guoweilong]

Are you using CGmapTools for BS-Seeker2's bam or Bismark's bam?

For BS-Seeker2's bam, CGmapTools will work well. For Bismark, you are suggested to use the command "cgmaptools convert bismark2cgmap".

Best, Weilong

在 2022-02-21 23:00:53，"freyayang" @.***> 写道：

Hi, I have the same issue with you. Do you figure out what's the problem? Thank you!

— Reply to this email directly, view it on GitHub, or unsubscribe. Triage notifications on the go with GitHub Mobile for iOS or Android. You are receiving this because you are subscribed to this thread.Message ID: @.***>

[freyayang]

Hi Weilong,

I used bs_seeker2-align.py to do the alignment, and the mappability is 58.9844% Aligning command line is below:
python /data1/program/BSseeker2/bs_seeker2-align.py -1 ZH11-1.cutadapt.1.fastq -2 ZH11-1.cutadapt.2.fastq -g /data1/ref/os/IRGSP.Nipponbare.fa --aligner=bowtie2 --bt2-p 7 -o ZH11-1.bsseeker.bam -d ./

Then I used bs_seeker2-call_methylation.py to call the methylation. But the count of reads showing C or T in CGmap file always lower than 4. See as below:

call methylation command line is below: python /data1/program/BSseeker2/bs_seeker2-call_methylation.py -d ./IRGSP.Nipponbare.fa_bowtie2/ -i ZH11-1.bsseeker.bam --rm-overlap -o ZH11-1

So now I try to call methylation with 'cgmaptools', but there is also some problems occurred which I asked under 'cgmaptools' issues.

Do you know any possible steps I may go wrong with BSseeker2? Thank you!!!