RNA-Seq AUTOMATIC workflows available/ make your own

Question

[Pin.Bioinf]

Hello, I am relatively new to RNA-Seq analysis, and Im wondering if people who do these kind of analysis have a workflow predefined or they just run trimming, mapping, quantification and DE analysis (for example) independently..

If there are workflows available, where can I find them? Or how could I develop my own? (bash maybe?) Ive been told about autoflow but I dont really understand the usage.

Thank you

[Buffo]

a good example, New protocolo tuxedo

Answer 1

[Santosh Anand]

For RNAseq differential Exp http://www.bioconductor.org/packages/3.7/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

Anything RNAseq https://rnaseq.uoregon.edu/