Hi,
I run into this problem when running BenchCT,
[checker] Reading info file
[checker] 160005484 alignment(s) read
[checker] 129001963 error(s) read
[checker] Reading junction bed file
Intervals must have positive width at /home/zingo/perl5/lib/perl5/CracTools/Interval/Query.pm line 46, <$fh> line 3.
My guess, BenchCT expects splices.bed.gz produced by SimCT to have start < end, which is not the case for junctions on antisense strand. The follwoing awk command seems to fix the problem, I appreciate any insight into this issue.
zcat splices.bed.gz | awk '{if ($6 == "+") {print $0} else {printf("%s\t%s\t%s\t%s\t%s\t%s\n", $1,$3,$2,$4,$5,$6)} }' | gzip > splices.modified.bed.gz
Thanks ~
Hi,
I run into this problem when running BenchCT,
My guess, BenchCT expects splices.bed.gz produced by SimCT to have start < end, which is not the case for junctions on antisense strand. The follwoing awk command seems to fix the problem, I appreciate any insight into this issue.
zcat splices.bed.gz | awk '{if ($6 == "+") {print $0} else {printf("%s\t%s\t%s\t%s\t%s\t%s\n", $1,$3,$2,$4,$5,$6)} }' | gzip > splices.modified.bed.gzThanks ~