About the sam flag for methylation extract about methyldackel HOT 3 CLOSED

Yes, that's how standard directional kits work for BS-seq.

from methyldackel.

Yes, that's how standard directional kits work for BS-seq.

Thanks very much. I have understood this problem.

And I have another problem about the flag. I found that for single-end read from PBAT protocol, SAM flag 0 and 16 in Bismark mean that this read is mapped to the forward strand and reverse complement strand, respectively. In MethylDackel , flag 0 and flag 16 mean that the read is from OT strand and OB strand, respectively. Is this right for PBAT reads? I think for PBAT reads, flag 0 means that the read is from CTOT strand, and flag 16 means that the read is from CTOB strand.

from methyldackel.

It's possible that bismark has changed how it handles flags with PBAT libraries, they didn't exist when either MethylDackel or bismark were created. If you're getting the wrong results from it then let me know and make a BAM file available for me.

from methyldackel.