Ribozero or polyA? Cant decide

Question

[datanerd]

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

[poisonAlien]

Since you mentioned its a discovery experiment, by doing ploy-A selection I think you will miss out most of lncRNAs.

Answer 1

[Asaf]

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)