search

atulkakrana / sPARTA

miRNA-target prediction and PARE-seq based validation tool - uses MapReduce model [Published]
Other
7 stars 7 forks source link

Cutting site for PARE result #7

Closed obenno closed 7 years ago

obenno commented 7 years ago

Hi Atul,

Thanks for the software~ There is one confusing thing, about of PARE validated cutting site. In the output file All.libs.validated.uniq.csv, by presenting genomeCleavePosition, do you mean that cleavage site is on the left or right of the reported site? Is it the same with positive and negative strand? Thanks~

Obenno

atulkakrana commented 7 years ago

Assuming that miRNA cleaved the RNA transcript (and not genome), the "genomeCleavePosition" refers to 5'-end of the cleaved transcript i.e. 5'-end of PARE reads. So, for genes on "watson" strand is must on left of the cleavage site and for "crick" strand it should be on the right of the cleavage site.

Atul

obenno commented 7 years ago

Thanks a lot ! That will be very helpful~~

Obenno