Impure Reads

[aob93]

Been using the tool and noticed some of my reads being discarded after being determined as impure.
I can't seem to find any further info regarding what determines a read as impure for a given repeat - any clarification would be greatly appreciated.

[pbsena]

hello,

we recently added some documentation on that warning in the puretarget tutorial here. This happens if you change the --min-read-quality flag, which is the case with the --preset targeted command. TRGT internally checks the sequence between flanks for reads with low rq value and discard the ones that are not composed of predominantly repetitive sequences. The detailed logic in the source code is here.