RNA-Seq single end 50 bp - will tophat Cufflinks/cuffdiff work for differential expression

Question

[oriolebaltimore]

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

[Brian Bushnell]

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.

[GenoMax]

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

[oriolebaltimore]

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

[GenoMax]

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

[GenoMax]

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