Comments (2)
from cgmaptools.
Thanks for your answer,
I looked at the input requirements of the documentation of cgmaptools bismark2cgmap
, but I found that I only generated the input of CpG, without CHG and CHH, as shown below:
After I removed --rmOverlap
, the program seemed to work fine, but I don't know if that makes sense. I would like to know after using bismark deduplicate_bismark
to deduplicate the bam file, if I use bam2cgmap to convert, do I still need to add --rmOverlap
?
I see quickstart write:
If it’s paired-end sequencing strategy, we recommend you add --rmOverlap to the above command to remove overlapped region of two mate reads avoiding twice consideration of the same DNA fragment.
Please forgive me that I don't quite understand the meaning of this sentence. I don't know if the bam after deduplication needs to be added --rmOverlap
from cgmaptools.
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