RNA-seq poly-A vs ribo minus

[Inti]

Hi guys,
I have been doing some RNA-seq experiments with polyA selected and ribo minus. Unfortunately after estimation of gene expression using cufflinks, cuffcompare etc., the overlap between the 2 methods is really low, just around 20% of the genes in common.
Has anybody done this kind of comparisons?
what would be most trustful polyA or ribo minus for gene expression.
thanks for your reply!

[hyjkim]

Hi guys,
I have been doing some RNA-seq experiments with polyA selected and ribo minus. Unfortunately after estimation of gene expression using cufflinks, cuffcompare etc., the overlap between the 2 methods is really low, just around 20% of the genes in common.
Has anybody done this kind of comparisons?
what would be most trustful polyA or ribo minus for gene expression.
thanks for your reply!

Hey Inti,

I worked on a paper that compared poly-a selection, ribominus and nugen. We found very high correlations between ribominus and poly-a selection. Please see this link for more details http://www.ncbi.nlm.nih.gov/pmc/arti...7/?tool=pubmed

[pmiguel]

Hey Inti,

I worked on a paper that compared poly-a selection, ribominus and nugen. We found very high correlations between ribominus and poly-a selection. Please see this link for more details http://www.ncbi.nlm.nih.gov/pmc/arti...7/?tool=pubmed

Nice work.

If the OP had a definition of "genes" that includes ones that produce non-polyadenylated transcripts, then a 20% "overlap" might be expected. Especially if the increased sequence space of the ribominus sample lowered its sensitivity to some, poorly expressed, poly adenylated messages.

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Phillip