Question

Expression Studies Of Alternative/Splice Variants Of A Gene

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11.7 years ago

jvknp ▴ 10

hi is there any sophisticated method (other than Real Time PCR) to study the expression of splice variants of a gene which differ by one or two codons

mrna • 2.9k views

ADD COMMENT • link updated 10.9 years ago by Biostar 20 • written 11.7 years ago by jvknp ▴ 10

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On StackOverflow this question would be closed as too open and vague. Suggest you improve it to avoid the same fate.

ADD REPLY • link 11.7 years ago by Neilfws 49k

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Elobarate your question...

ADD REPLY • link 11.7 years ago by aravind ramesh ▴ 540

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I was studying the relative abundance of two splice variants (mRNA) under different stress conditions by qPCR. These two splice variants differ by one codon (revealed by RNA-seq data).

ADD REPLY • link 11.7 years ago by jvknp ▴ 10

score 2 · Answer 1 · 2013-03-27

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11.7 years ago

Steve Lianoglou 5.2k

I'm not sure what you are really asking ("sophisticated method" is a bit vague), but there are several approaches to study changes in splicing using RNA-seq data, such as:

DEXSeq: R | Publication
BitSeq: Python | R | Publication
Cufflinks: Software | Publication

ADD COMMENT • link 11.7 years ago by Steve Lianoglou 5.2k