I recently started to work with
shoremap (mainly because my collaborators requested so) in order to pinpoint ems mutations in an Arabidopsis line they created.
While the majority of the protocol runs successful , I'm in doubt about which scoring matrix to use in the
shore consensus step. It seems that there are two available :
scoring_matrix_het.txt . Though I extensively searched the internet and shore manuals and papers I can not seem to find any decent explanation when to use which one. In the manual of shore they mostly use the
_hom one , while in the shoremap manual they use the
_het one (in the shore part of the protocol).
It concerns a backcross analysis here but any info for the outcross approach would also be appreciated.
I would be grateful if someone has any insights on this they want to share.