Error: Unable to determine variant sequence. Conflicting (overlapping) variant sequences present.

[sidsrivastava001]

Hi!

Trying to run ShapeMapper on two fastq files (SRR1534952 and SRR1534954) and ran into this "variant overlapping" error. I have pasted the error message as well as my command here. Any ideas why this might be happening?

[Psirving]

Hi, I'm not 100% sure about how the logic of this step works, but it is meant to be provide a single "correct" reference sequence for downstream steps. I think shapemapper throws this error if it identifies conflicting variants, which (I think) is a location that differs from the provided sequence but has multiple possible "correct" sequences.

FYI, I looked at these SRA entries. It looks like these are both icSHAPE prepared libraries, which is distinct from SHAPE/DMS-MaP in that the signal is contained in RT stop events rather than mutations. ShapeMapper2 will not provide accurate reactivity profiles for this type of data.