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Old 03-15-2012, 01:53 PM   #1
himanshu04
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Location: New York

Join Date: Mar 2012
Posts: 35
Default RNA-seq pipeline

Hey everyone,
I am new to this field and I am really interested in learning more about it. I have a project to do in which, I have RNA-seq data and I have to do the following:
1.how do you think you would try to go about figuring out how to identify short non-coding versus coding transcripts?- I think this could be done by doing a Blast x using Blast2go.
2.How would you try to identify translocations/alternative splice variants? - I am not very sure about this one but should I be finding out the differential expression or protein isoforms for this using Tophat and Cufflinks.??
3.Then to validate your results, to obtain statistical significance? - I think I would have to use Bioconductor packages DEseq/edgeR.
Also, can anyone give a better suggestion or some guidelines/steps for the same. Any help is much appreciated.
Thanks.
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