Selection of RNA-Seq appropriate tools for meta-analysis

Question

[Sitara]

Hello all,

I am running a meta-analysis with publicly available RNA-seq data, containing multiple samples which have approximately 5000 replicates each. I want to compare these samples and get the top genes which are up-regulated and down-regulated.

Can someone suggest me Which combination of tools from the below will be appropriate?

Hisat-StringTie-Ballgown
Hisat-HTseq-DESeq
STAR-HTseq-DESeq

Any other suggession will be appreciated.

Thanks in advance.

Answer 1

[Devon Ryan]

With that many samples you'll want salmon or kallisto instead, likely followed by tximport/limma (limma simply because it'll be a lot more performant with such a large number of samples).

[Sitara]

Thanks for your suggestion, will try to implement it.