perRead output - print Bismark methylation call string?

[embertucci]

Hi Devon,

I've been using MethylDackel's perRead function to investigate methylation discordance patterns within each read and I was wondering if there is a way to print the methylation call string from Bismark for each read along with the other perRead output? I'm trying differentiate between patterns occurring within reads with same number of methylated/un-methylated cytosines (i.e. ZZZz vs. ZZzZ) . Thanks in advance for your help and thank you for developing such great tool!

Best,
Emily

[dpryan79]

There's no option for that at the moment, since most other BS-seq aligners don't produce that information. I guess I could add it if it's there. What's that tag called again?

[embertucci]

It's the methylation call string (column 8 in the Bismark SAM output)

[abcoxyzide]

Hi Devon; not sure if I should piggyback on this or raise a new issue.

I have a similar request if you're planning to work on this - do you think you can output other properties of the reads as well, along with the methylation information? I am particularly interested in the FLAG value (mainly for distinguishing OT/OB) and insert size.