Question: RNA-seq analysis data analysis pipeline
gravatar for mohammedtoufiq91
4 months ago by
mohammedtoufiq9140 wrote:


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

ADD COMMENTlink modified 4 months ago by Bastien Hervé4.3k • written 4 months ago by mohammedtoufiq9140

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.

ADD REPLYlink written 4 months ago by ATpoint18k
gravatar for Philipp Bayer
4 months ago by
Philipp Bayer6.1k
Philipp Bayer6.1k wrote:

I suggest the Hisat2/Stringtie/Ballgown pipeline, see Dave Tang's blogpost:

For read cleaning and adapter trimming, have a look at fastp:

ADD COMMENTlink written 4 months ago by Philipp Bayer6.1k
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