bismark deduplicated BAM

[biozzq]

Hi,

I used Bismark to analysis WGBS, including alignment, remove duplication, methylation extractor. In order to use your pipeline (methpipe), I used format_reads to generate the compatible SAM file (format_reads -o SAM -f bismark bismark_deduped.bam). Then, I ran duplicate-remover to remove duplication again. In my mind, as the PCR duplicates have been removed by Bismark, the duplication rate should be very low when analyzing with duplicate-remover. I do not know if 2.15761 is appropriate here.

Also, I found that the single-site methylation levels and coverage are some different between bismark_methylation_extractor and methcounts. I do know how to explain this.

chr	pos	Bismark_rate	Bismark_coverage	methpipe_rate	methpipe_coverage
1	605488	71.42857143	7	0.882353	17
1	605494	71.42857143	7	0.875	16
1	605496	85.71428571	7	0.777778	18
1	634551	86.20689655	29	0.577778	45
1	755058	88.88888889	9	1	12
1	774718	100	17	0.952381	42
1	776324	87.5	8	1	17
1	778068	100	19	0.757576	33
1	778443	0	11	0	24
1	778631	0	12	0	25
1	778758	0	5	0	18
1	778788	0	6	0	18
1	778974	0	7	0	10
1	779024	0	7	0	13
1	779576	100	5	1	17
1	780010	100	18	1	25
1	780567	100	12	1	12
1	780669	100	10	0.916667	12
1	787711	100	24	1	37
1	796794	93.75	16	1	40
1	819364	100	18	1	31
1	830251	100	14	1	25
1	835549	100	5	1	8
1	840855	91.66666667	24	0.95	40
1	841218	100	10	1	28

Looking forward to your reply, thanks. Yours sincerely.

Zheng zhuqing

[andrewdavidsmith]

This is a question regarding software from others. Send me this by email please.

[andrewdavidsmith]

@biozzq I'm closing this due to inactivity. Again, if you want me to comment on what software written by others is doing, please contact me directly.