RNA-seq analysis data analysis pipeline

Question

[mohammedtoufiq91]

Hi,

We have generated a set of RNA-seq samples from blood tissue (non globin depleted). These are human paired-end samples with read length of 150bp. I would like to find out the differentially expressed genes and perform fold change comparison between the different subjects. Please assist me with the most appropriate tool that can be utilized from alignment to the differential expression analysis including (Pre and Post QA/QC, Trimming, Alignment, Filtering, Quantification (both gene and transcript), Differential Expression, and Fold Change).

Thank you, Toufiq

[ATpoint]

Please use the search function. This has been asked and addressed many times before. See also enter link description here. My preferred pipeline, containing only well-maintained tools would be Salmon-DEseq2.

Answer 1

[Philipp Bayer]

I suggest the Hisat2/Stringtie/Ballgown pipeline, see Dave Tang's blogpost: https://davetang.org/muse/2017/10/25/getting-started-hisat-stringtie-ballgown/

For read cleaning and adapter trimming, have a look at fastp: https://github.com/OpenGene/fastp