Determine whether reads are from PBAT automatically

[andrewdavidsmith]

This should be easy, based on analyzing the nucleotide composition of a collection of reads at the start of the file (e.g. 100k reads).

[bdecato]

I think you're right that we can detect it computationally, but is that true in all cases?

Bismark has an explicit --pbat option and fails silently if you try mapping PBAT reads without it. What if we implement the nucleotide analysis function and print a warning if the composition doesn't match up with the flag?

[mengzhou]

I have another question: do we still need the AG_WILDCARD option for mapping single-end? The reads are the same for single-end PBAT.

[mengzhou]

GSE86903
This dataset has mixed WGBS and PBAT protocols. Specifically, BS-seq_H9_hEpiLC_d4_1 and BS-seq_H9_hEpiLC_d4_2 are WGBS, while others are PBAT. Should be a good one to test this.