Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: Selection of RNA-Seq appropriate tools for meta-analysis
0
gravatar for Sitara
2.6 years 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 • 584 views
ADD COMMENT • link •
modified 2.6 years ago by Devon Ryan ♦ 98k • written 2.6 years ago by Sitara • 0
3
gravatar for Devon Ryan
2.6 years ago by
Devon Ryan ♦ 98k
Freiburg, Germany
Devon Ryan ♦ 98k 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 2.6 years ago by Devon Ryan ♦ 98k

Thanks for your suggestion, will try to implement it.

ADD REPLY • link written 2.6 years ago by Sitara • 0
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1605 users visited in the last hour
_