Hi, It took me a while, but I was confused by getting different results when using 'which' in reading BAM files. In my use case, I have a GRanges with 15 ranges (different exons from the transcripts of a gene) and I get much higher coverage values than simply using the range of the 15 ranges.
I now realize that by using all 15 ranges I was duplicating the number of alignments to use for calculating the coverage instead of what I wanted: get all the reads that mapped to any of the 15 ranges counting them once each. You could say that as a user I was incorrectly using the function. Or that it would be good to clarify that if you use overlapping ranges in 'which' then you could read a sequence read more than once. Anyhow, I think that clarifying would be useful to others in the future. Even a simple example could show this situation so others are aware. The code and output is available at https://gist.github.com/lcolladotor/76f2efdd5d5108772696 Cheers, Leo _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
