how do Differential gene expression analysis by Salmon output
Hello,
I did transcript quantification by Salmon. now I have an output like this table;
Name Length EffectiveLength TPM NumReads
ENSMUST00000193812.1 ENSMUSG00000102693.1 OTTMUSG00000049935.1 OTTMUST00000127109.1 RP23-271O17.1-001 RP23-271O17.1 1070 TEC 1070 885.998 12.758544 75.864598
ENSMUST00000082908.1 ENSMUSG00000064842.1 - - Gm26206-201 Gm26206 110 snRNA 110 27.847 0 0
ENSMUST00000162897.1 ENSMUSG00000051951.5 OTTMUSG00000026353.2 OTTMUST00000086625.1 AC157543.1-003 Xkr4 4153 processed_transcript 4153 3968.998 0.384028 10.229377
ENSMUST00000159265.1 ENSMUSG00000051951.5 OTTMUSG00000026353.2 OTTMUST00000086624.1 AC157543.1-002 Xkr4 2989 processed_transcript 2989 2804.998 4.503059 84.770623
ENSMUST00000070533.4 ENSMUSG00000051951.5 OTTMUSG00000026353.2 OTTMUST00000065166.1 AC157543.1-001 Xkr4 3634 protein_coding 3634 3449.998 0 0
ENSMUST00000192857.1 ENSMUSG00000102851.1 OTTMUSG00000049958.1 OTTMUST00000127143.1 RP23-317L18.1-001 RP23-317L18.1 480 processed_pseudogene 480 314.826 0 0
ENSMUST00000195335.1 ENSMUSG00000103377.1 OTTMUSG00000049960.1 OTTMUST00000127145.1 RP23-317L18.4-001 RP23-317L18.4 2819 TEC 2819 2634.998 1.92262 34
ENSMUST00000192336.1 ENSMUSG00000104017.1 OTTMUSG00000049961.1 OTTMUST00000127146.1 RP23-317L18.3-001 RP23-317L18.3 2233 TEC 2233 2048.998 0 0
I want to do differential gene expression analysis by DESeq2 on this output and on the basis of Gene_id and NumReads columns, I am not sure actually if aggregated gene name based on gene_id is correct? do you have any suggestion about that? how do DGE analysis on?
Thanks in advance
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Take a look at the
tximportpackageTake a look at section 2.1 in RNASeqGene workflow for
DESeq2. Detailed information in thistximportvignette.thanks, don't you have any suggestion except tximport, because I am new in R and I can't use it, can I use aggregate option to sum genes ?"
Sure you can, it's well documented
Please embrace the opportunity to learn a new skill, lkianmehr. In my vocabulary, at least, the phrase "I can't" does not exist.
Make a start from Here.
I could learn it! thanks for giving motivation