Dear All,
Should cufflinks also include a closure-search option that is included with TopHat?
tophat has;
-r/--mate-inner-dist = distance between paired end reads
--mate-std-dev = std deviation of this distance
and an option to deal with overlapping reads from paired ends
--closure-search
Likewise cufflinks has;
-m = distance between paired end reads
-s = std deviation of this distance
But there is no closure search in cufflinks. As I see overlapping reads in my data and I assume it has happened to other peoples datasets, should cufflinks also have a closure search like tophat?
Should cufflinks also include a closure-search option that is included with TopHat?
tophat has;
-r/--mate-inner-dist = distance between paired end reads
--mate-std-dev = std deviation of this distance
and an option to deal with overlapping reads from paired ends
--closure-search
Likewise cufflinks has;
-m = distance between paired end reads
-s = std deviation of this distance
But there is no closure search in cufflinks. As I see overlapping reads in my data and I assume it has happened to other peoples datasets, should cufflinks also have a closure search like tophat?