Hello Jianguang,
In simple terms, No produces a strict alignment and Yes produces a
more permissive alignment.
The option 'Allow indel search:' is a way of allowing for variability in
your data (presumably biologically valid) to not be interpreted as
mismatches or gaps. Mismatches/gaps in
Dear All,
I want to compare the pre-mRNA alternaive splicing events between RNA-seq
datasets. Do I need to allow indel search when I run Tophat? What is the indel
search for? I could not find detail information about indel search through
the documentation of Tophat.
Thanks.
Jianguang Du
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