Question: how do Differential gene expression analysis by Salmon output
gravatar for lkianmehr
9 weeks ago by
lkianmehr30 wrote:

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

ADD COMMENTlink modified 9 weeks ago by genomax59k • written 9 weeks ago by lkianmehr30

Take a look at the tximport package

ADD REPLYlink written 9 weeks ago by WouterDeCoster35k

Take a look at section 2.1 in RNASeqGene workflow for DESeq2. Detailed information in this tximport vignette.

ADD REPLYlink modified 9 weeks ago • written 9 weeks ago by genomax59k

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 ?"

ADD REPLYlink written 9 weeks ago by lkianmehr30

because I am new in R and I can't use it,

Sure you can, it's well documented

ADD REPLYlink written 9 weeks ago by WouterDeCoster35k

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.

ADD REPLYlink written 9 weeks ago by Kevin Blighe33k

I could learn it! thanks for giving motivation

ADD REPLYlink written 8 weeks ago by lkianmehr30
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