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Posts by mammana
Answer: A: bamCount paired.end arg
... Hi Kasia, thanks for your question and sorry for answering only now (I didn't get any notification...). That's correct, the bamCount function does not have the option paired.end="extend". It wouldn't make sense, because bamCount counts the 5' end of a read, so if you extend it to the whole fragmen ...
... Thanks for the post. To insert NAs for those GRanges in chromosomes that are not in the header of the bam file is a solution I already thought about. It is probably not a very clean solution, but on the other hand changing the header of bam files is much more time consuming. So I will add this featu ...
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