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Question: Selection of RNA-Seq appropriate tools for meta-analysis
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gravatar for Sitara
12 months ago by
Sitara • 0
Sitara • 0 wrote:

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.
rna-seq alignment • 299 views
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modified 12 months ago by Devon Ryan ♦ 90k • written 12 months ago by Sitara • 0
3
gravatar for Devon Ryan
12 months ago by
Devon Ryan ♦ 90k
Freiburg, Germany
Devon Ryan ♦ 90k wrote:

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).
ADD COMMENT • link written 12 months ago by Devon Ryan ♦ 90k

Thanks for your suggestion, will try to implement it.

ADD REPLY • link written 12 months ago by Sitara • 0
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