Question: Searching For A Simple Yet Powerful Workflow For Rna-Seq
6
gravatar for Sukhdeep Singh
5.3 years ago by
Sukhdeep Singh8.9k
Netherlands
Sukhdeep Singh8.9k wrote:

Hi, I have to start working with RNA-Seq data and have worked previously with ChIP-Seq so I am familiar with mapping, coverage, visualizations and tools etc. Could you guys please tell me a simple workflow (published/unpublished) for the analysis of RNA-Seq data, analysing the gene expression between a wild type and knockout sample. I tried rseq, galaxy (which is good) and GENE-Counter, still I am not confident with my analyses and I get lost in the downstream analyses. Could you recommend a good review and pipeline to start with!!

Thanks a lot

workflow pipeline rna-seq • 5.3k views
ADD COMMENTlink modified 5.0 years ago by ngsgene350 • written 5.3 years ago by Sukhdeep Singh8.9k
6
gravatar for Sameet
5.3 years ago by
Sameet290
Sameet290 wrote:

You probably want to look into the following paper. Nature Protocol Paper

ADD COMMENTlink written 5.3 years ago by Sameet290
1

It's a really good review!! ... but instead of Tophat I prefer to use other Cufflinks-compatible mappers, like MapSplice or GSNAP.

ADD REPLYlink written 5.3 years ago by Geparada1.2k

+1 for Cufflinks and MapSplice.

ADD REPLYlink written 5.3 years ago by Khader Shameer17k

I fact, now I'm going to try MapSplice 2.0 wich support multi-threads!

ADD REPLYlink written 5.3 years ago by Geparada1.2k

Is there any major difference b/w MapSplice and Tophat, Also, some people use bwa to map the reads to a custom splicejunction library, I think all of them serve the same purpose, or is there any significant difference b/w them!!

ADD REPLYlink written 5.3 years ago by Sukhdeep Singh8.9k

Looks good, I am reading it. Thanks

ADD REPLYlink written 5.3 years ago by Sukhdeep Singh8.9k
4
gravatar for ngsgene
5.3 years ago by
ngsgene350
United States
ngsgene350 wrote:

This is a well detailed wiki for RNA-Seq analysis

http://seqanswers.com/wiki/How-to/RNASeq_analysis

ADD COMMENTlink written 5.3 years ago by ngsgene350

Thanks looks good

ADD REPLYlink written 5.3 years ago by Sukhdeep Singh8.9k
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