Hi
I would like to identify pairs in RNA seq that dot not map properly. In particular, I am interested on this kind of pattern:
--->---------- R1
---------->--- R2
instead of
--->---------- R1
----------<--- R2
which I believe i can identify in the sam using the flag: read reverse strand or mate reverse strand
After running STAR I have a staggering 100% properly paired flag. I wonder if STAR per default only report properly paired read. If there is a way using STAR or any other tools to achieve this?
I believe in desperation I have the option to align R1 and R2 individually, but that incurs a lot of post precessing. And I would rather not reinvent the wheels.
I greatly appreciate your help, Romain
•
written
by
romain.lannes
1 answer
There are definitively tools out there to call structural variants, including inversions. I am not sure if RNA-seq data is the appropriate input, since most tools are likely written for WGS data, but InvBFM could work nonetheless ?!? Also see this example to extract discordant pairs.
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