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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