I used tophat to align paired-end 76bp RNA-seq.
The fragments selected at 300bp.
As the example in tophat manual shows- I used: tophat -r 148 ...
When I inspected the .bam with:
samtools view accepted_hits.bam
or- samtools faststat accepted_hits.bam
I relized that none of the reads was align with correct insert size.
1. What to put as insert?
2.what is the best size of the std. to put in --mate-std-dev ?
Thanks in advance,
Oz
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