[miso-users] How to run MISO with ENSEMBL GTF if reads were aligned against UCSC genome

[Anil Kesarwani]

Hi,

I aligned reads against UCSC genome using STAR, where UCSC gtf was used as
reference annotation. However, I want to do quantitation of splicing event
as per in ENSEML gtf file using MISO tool.  In the homepage of MISO, it has
been suggested to re-align the reads with the genome build prepared with
ENSEMBL, in order to do so.

My question is that if only the chromosome naming convention is different
between UCSC and ENSEMBL, then just by changing the chromosome name in
ENSEMBL gtf file as per in UCSC should be sufficient. Why I should need to
re-align the whole reads.

I will highly appreciate if someone could help me out.

Thanks.


Best,

Anil
*Anil Kumar Kesarwani*
*Postdoctoral Associate*

Yale Cancer Center
Section of Hematology
300 George Street, # 786B
New Haven CT 06510

Office : +1 203 737 6990
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