May I use numreads for doing DGE after quantifying by Salmon

Question

[lkianmehr]

Hello,

I have quantified piRNA and tRNA of RNA-seqs by Salmon on fasta file, now to do DGE analysis may I use numreads ?

[ATpoint]

Cross-posted on BioC: Question: quantifying piRNA and tRNA by Salmon

Answer 1

[WouterDeCoster]

For using salmon output with differential expression analysis, take a look at tximport

[sangram_keshari]

Yes, this pipeline is a better choice.

[lkianmehr]

but I taught that tximport should be used just for summarizing transcript_id to gene_id

[sangram_keshari]

Yes, but also it has few functions for a seamless integration with few outputs from other packages:

According to that Bioconductor vignettes link shared by @WouterDeCoster:

the tximport pipeline offers the following benefits: (i) this approach corrects for potential changes in gene length across samples (e.g. from differential isoform usage) (Trapnell et al. 2013), (ii) some of the upstream quantification methods (Salmon, Sailfish, kallisto) are substantially faster and require less memory and disk usage compared to alignment-based methods that require creation and storage of BAM files, and (iii) it is possible to avoid discarding those fragments that can align to multiple genes with homologous sequence, thus increasing sensitivity (Robert and Watson 2015).

Answer 2

[sangram_keshari]

Basically, NumReads will have quantified reads mapped to each transcript. Yes, you can use them.

Once quantified, You can use other tools like - edgeR and DESeq2 for DEG.