Hi All,
This is a very simple question, or should be, but there seems to be some confusion out there.
My understanding is that insert size is the number of bases between paired end reads (example: 300 bp fragments, 2*75 reads -> insert size 150). However, looking trough different threads here and information elsewhere the fragment is sometime referred to as insert as well, making insert size == fragment size.
I wonder whether different programs (BWA, picards CollectInsertSizeMetrics, bfast, samtools etc) have different definitions of insert size, which might make things messy. Right now I am especially interested in picards definition.
Any ideas?
Thanks,
Boel
This is a very simple question, or should be, but there seems to be some confusion out there.
My understanding is that insert size is the number of bases between paired end reads (example: 300 bp fragments, 2*75 reads -> insert size 150). However, looking trough different threads here and information elsewhere the fragment is sometime referred to as insert as well, making insert size == fragment size.
I wonder whether different programs (BWA, picards CollectInsertSizeMetrics, bfast, samtools etc) have different definitions of insert size, which might make things messy. Right now I am especially interested in picards definition.
Any ideas?
Thanks,
Boel
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