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Old 01-20-2015, 08:20 AM   #3
Location: paris

Join Date: Jan 2013
Posts: 10

well i don't really care about the sequence, it's for profile comparison.
as long as the positions are right, i'm ok with it.

maybe i shouldn't have called it pileup, but coverage. just a measure of how many reads overlap each position, in order to be able to compare profiles at certain loci (such as transcriptional readthrough for example).

for future reference, i discovered a script that does more or less this in the "misc" folder of samtools. it's called

i'll check it more in detail and report back.
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