Question on secondary and supplementary reads about methphaser HOT 4 CLOSED

Usually using supplementary and secondary alignment can cause methylation reading errors. MethPhaser will output errors if you use secondary and supplementary alignments.

from methphaser.

Yep, I agree. But my point is about re-introducing those reads AFTER running methphaser before assembling.

from methphaser.

I would advise not to do that because MethPhaser flip the phaseblocks and flip the reads' haplotype assignments when it finds the relation between two neighbor phaseblocks are flipped. i.e., HP1 in phaseblock 1 is the same to HP2 in phaseblock2. Reintroducing those reads might be not optimal.

from methphaser.

Thanks for explaining, I see your point!

from methphaser.