4.9 years ago by
Not sure, but if you have a bam file and samtools you can find the depth of coverage using the
$ samtools depth in.bam -r 1:100-200
It will print out a per-base pair depth of coverage, which can be normalized to the average coverage of the sample. So if the reads in the region have twice the coverage they are duplicated ( a normalized value of 1.5, as 0.5 is a heterozygous deletion)
You can perform the same task with
$ samtools view -c in.bam 1:100-200
and normalize by (read count / region size) * average read length / average coverage
Doing it systematically for RNA-seq I'm not sure, but you can probe around your bam files and see if there is an amplification.