Ribozero or polyA? Cant decide
Hi all,
Does anyone have recommendations / articles on deciding between poly a and ribo zero RNA-seq experiment? Pros cons? The more i read, the confused I get as to what might help my dataset better.
This is more of a discovery experiment and its comparative not necessarily differential expression.
Thanks so much in advance!!
Mamta
1 answer
Some pros of poly-A:
- Coverage of mRNA is more uniform than with RiboZero (there is, however, a 3' end bias in poly-A)
- You won't get tRNAs which take up a lot of reads - depends on the size selection in the library prep.
A con of poly-A:
- You won't get non poly-A'd RNAs (again - size selection plays another role here)
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Since you mentioned its a discovery experiment, by doing ploy-A selection I think you will miss out most of lncRNAs.