Single-cell RNA-seq : for what questions ? and what are the classical pipelines ?

Question

[schmilblik]

Hello stars!

I'm trying to find out a little bit about single cell RNA-seq and I want to know in which context (the major problems that this technique can answer) and what are the pipelines used in general when we have both classical RNA-seq AND single-cell RNA-seq data?

Thanks in advance

Answer 1

[vivekbhr]

Hi

This recent review might be useful to you..

Answer 2

[Shicheng Guo]

• STAR: ultrafast universal RNA-seq aligner
• TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
• Cufflinks: Transcriptome assembly and differential expression analysis for RNA-Seq.
• Trinity: a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data
• SpliceMap: SpliceMap is a de novo splice junction discovery tool
• Degust: User friendly RNA-seq differential expression analysis with Degust