[Useq-users] RNA-IP analysis with Useq

[mali s. <sha...@gm...>]

Dear Useq-users
Is it possible to analyse RNA-IP data using Useq?
I have IP and Input data from RNA that was fragmented to 100nt, and then
treated with an antibody against a specific RNA methylation.
I aligned reads to the genome (I don't care of junctions reads, and only
10% of the data couldn't be mapped to the genome), and I would like
to find enriched regions in IP compared to Input.
The idea is similar to ChIP-seq, but I'm wondering if there are special
issues I should taking care of since the reads are coming from the
transcriptome and not the genome.
For example, in ChIP-seq finding tools like MACS and others, I should give
as parameter the effective genome size.
When I run MACS (sorry I haven't tried Useq with this data yet) with
gsize=transcriptome size, I get ~2000 peaks, however, when I run it with
gsize=genome I get ~22000 peaks. In a genome browser, those peaks that were
missed with smaller gsize look real by looking them in a genome browser and
comparing them with their Input. Hence I thought of finding a tool that can
compare IP directly to Input without taking into account a random
expectations calculated based on the genome size. Is it make sense? Is it
possible to do it with Useq?
Looking forward to your reply
Thanks
Mali