Question: May I use numreads for doing DGE after quantifying by Salmon
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gravatar for lkianmehr
4 months ago by
lkianmehr30
France
lkianmehr30 wrote:

Hello,

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

dge salmon • 200 views
ADD COMMENTlink modified 4 months ago by WouterDeCoster37k • written 4 months ago by lkianmehr30

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

ADD REPLYlink written 4 months ago by ATpoint14k
1
gravatar for WouterDeCoster
4 months ago by
Belgium
WouterDeCoster37k wrote:

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

ADD COMMENTlink written 4 months ago by WouterDeCoster37k

Yes, this pipeline is a better choice.

ADD REPLYlink written 4 months ago by sangram_keshari130

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

ADD REPLYlink written 4 months ago by lkianmehr30

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).

ADD REPLYlink written 4 months ago by sangram_keshari130
0
gravatar for sangram_keshari
4 months ago by
sangram_keshari130 wrote:

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.

ADD COMMENTlink modified 4 months ago • written 4 months ago by sangram_keshari130
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