Entering edit mode
8.9 years ago
Vladimir Bajić
▴
20
Hi,
I was running CollectInsertSizeMetrics
on the output file from Bowtie2 and changing the parameter DEVIATIONS I got totally different results for MEAN_INSERT_SIZE
and for STANDARD_DEVIATION
.
e.g.
for DEVIATIONS=200.0
- MEAN_INSERT_SIZE = 2302,200903
- STANDARD_DEVIATION = 1026,875768
for DEVIATIONS=10.0 (default)
- MEAN_INSERT_SIZE = 491,421658
- STANDARD_DEVIATION = 338,674711
(data: Illumina mate pair with, as company said, insert size of 3kb)
So, I would like to know which value should I set up for DEVIATIONS and how one decide which value to use?
Thank you!
Vlad