How to start Differential gene expression analysis ?

Question

[sunnykevin97]

Hi

After denovo assembly, the assembled transcripts were quantified using salmon it generated a quant.sf file

can I use this file as an input for differential gene expression analysis using edgeR ?

I had more than ~100 samples to analyze,

Can you provide some good tutorial easily understandable, very new to bioinformatics research.

Suggestions Please!

head quant.sf
Name    Length  EffectiveLength TPM NumReads
TRINITY_DN30552_c0_g1_i1    772 523.000 2.826146    133.000
TRINITY_DN30585_c0_g1_i1    572 323.000 0.756946    22.000
TRINITY_DN30563_c0_g1_i1    516 267.000 56.484784   1357.057
TRINITY_DN30563_c0_g2_i1    515 266.000 382.614124  9157.943
TRINITY_DN30577_c0_g1_i1    1130    881.000 1.337133    106.000
TRINITY_DN30527_c1_g1_i1    366 117.000 3.035056    31.953
TRINITY_DN30527_c0_g1_i1    446 197.000 4.343794    77.000
TRINITY_DN30562_c0_g1_i1    236 16.266  4.099455    6.000
TRINITY_DN30526_c0_g1_i1    384 135.000 1.399458    17.000

[Ram]

Have you searched online for "differential expression salmon"? That would have shown you this comment by genomax on a previous question that addresses your problem.

Answer 1

[ATpoint]

The output of salmon are transcript level abundance estimates. These should be aggregated to the gene level (so gene counts, not transcript counts/abundances because edgeR and company perform gene level differential analysis) e.g. with the tximport package from Bioconductor and then analyzed with edgeR. Both tximport and edgeR have comprehensive manuals with a lot of example code, please read them extensively.

[sunnykevin97]

tximport seems to be very hard for me to understand, some simple example to understand.

[ATpoint]

Read https://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html and linked references