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10-14-2011, 08:25 AM
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#1 |
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Member
Location: Mexico city Join Date: Jul 2008
Posts: 12
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RNA-seq poly-A vs ribo minus
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! |
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10-18-2011, 12:24 PM
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#2 | |
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Member
Location: Santa Cruz Join Date: Apr 2010
Posts: 18
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Quote:
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 |
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10-18-2011, 01:23 PM
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#3 | |
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Senior Member
Location: Purdue University, West Lafayette, Indiana Join Date: Aug 2008
Posts: 2,317
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Quote:
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. -- Phillip |
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