Hi All,
I have been trying to count the number of RNA-seq reads that fall into the
various Cufflinks class codes ('=', 'j', 'u', 'x', etc...) and I am curious
how others are determining how to count reads per class..

I tried first using the BedTools tool where you "count" the number of reads
overlapping another set of intervals and later realized that each interval
is extended1 kb up and downstream prior to the analysis (by default and not
adjustable on Galaxy), so the number of reads that were "counted" for all
of the classes was always much more than the amount of reads that I had for
my Bam file. I then tried to isolate reads from each class into separate
BAM files, using the BedTools "intersect" tool and there I consistently end
up with significantly less reads than I have in my sample.

I am very curious to find out how others are tackling this problem on

Thanks for any input!

Mo Heydarian
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