Question: RNA-Seq single end 50 bp - will tophat Cufflinks/cuffdiff work for differential expression
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gravatar for oriolebaltimore
4.0 years ago by
United States
oriolebaltimore160 wrote:

Dear group, I have single end 50bp RNA-seq library for two different cell populations. I like to identify the deferentially expressed genes between these two cell types. Is Tophat - Cufflinks - Cuffdiff pipeline a suggested option or one should use STAR-alignment - HT-Seq - DESeq2 - is the ideal option?

appreciate your suggestions. Thanks Adrian

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by oriolebaltimore160
1

I wouldn't necessarily say it's ideal, but of the two, I'd suggest the second - staying away from the Tuxedo pipeline is generally a good idea, in the interests of speed, stability, and accuracy.

ADD REPLYlink written 4.0 years ago by Brian Bushnell17k

Any modern (splice aware, if you expect splicing to be present) aligner followed by featureCounts and DESeq2 should be fine.

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by GenoMax94k

Thank you. How do I specify stranded (fr-firststrand (from dUTP)) to STAR. I cannot find the command to specify strandedness to STAR.

Thanks Adrian

ADD REPLYlink written 4.0 years ago by oriolebaltimore160

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keeps threads logically organized.

ADD REPLYlink written 4.0 years ago by GenoMax94k

See this post: C: Strand-specific vs. non-strand-specific RNAseq

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by GenoMax94k
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