Closed re2srm closed 5 years ago
Hi there,
Thanks for your interest in our software! Yes that should be correct for the library size - I also wanted to comment on your previous post before you closed it, but you should probably run each file with a separate output destination if you are running jobs in parallel because (as you said) the outputs might conflict in some way within in the pair_1 and pair_2 folders.
Best, Nick
Great. Thanks a lot.
Hello,
Just needed a small clarification regarding normalising the counts generated by repenrich. The tutorial mentions that library size should calculated as reads processed - reads that failed to align using the bowtie log. I am a little confused about how to calculate this. Here is the bowtie result for one of my sample:
26562723 reads; of these: 26562723 (100.00%) were paired; of these: 7376294 (27.77%) aligned concordantly 0 times 7786417 (29.31%) aligned concordantly exactly 1 time 11400012 (42.92%) aligned concordantly >1 times
86.54% overall alignment rate
Since the total alignment rate is 86.54% I am assuming I would use 0.8654*26562723=22987380 as the library size. Am I correct?
Thanks