Hi all,
I am trying STAR to analyze my RNAseq and it seems that, when a read is on an exon-exon junction, STAR fills up the read with N (then it increases the size of the read). My problem is when I want to use genomeCoverageBed to get the per base coverage, the output is a lot of reads in the different introns.
Do you know if there is a way to change the output of STAR (I didn't see anything but maybe I went too fast on the manual), like splitting the read into two reads and for each of them the starting and ending positions?
Thanks in advance.
S.
I am trying STAR to analyze my RNAseq and it seems that, when a read is on an exon-exon junction, STAR fills up the read with N (then it increases the size of the read). My problem is when I want to use genomeCoverageBed to get the per base coverage, the output is a lot of reads in the different introns.
Do you know if there is a way to change the output of STAR (I didn't see anything but maybe I went too fast on the manual), like splitting the read into two reads and for each of them the starting and ending positions?
Thanks in advance.
S.
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