Question: (Closed) DESeq2: Differential gene expression
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gravatar for umeshtanwar2
6 weeks ago by
umeshtanwar210
umeshtanwar210 wrote:

Hi all

I am working on the RNAseq data of Arabidopsis thaliana. I have done the differential gene expression analysis by using DESeq2. Now I have a list of DE genes (gene ID) in csv file. How can I have the names and description of the genes in my DE genes results file? My file looks like this:

baseMean    log2FoldChange  lfcSE   stat    pvalue  padj
gene:AT5G65080  122.875394083372    1.69474723920958    0.145231051625416   11.7004967984981    1.26709498309877E-31    5.85423224091292E-28
gene:AT1G64380  168.896650212747    1.30834505764162    0.132353055400632   9.78909978664265    1.25407410840269E-22    2.41419716485088E-19
gene:AT5G65070  82.6936482493549    1.26016444752325    0.14553940276928    8.66897373013599    4.36032539676582E-18    3.59742417823883E-15

My annotation file (GTF) looks like this:

1   araport11   exon    3631    3913    .   +   .   transcript_id "transcript:AT1G01010.1"; gene_id "gene:AT1G01010"; gene_name "NAC001"; Name "AT1G01010.1.exon1"; constitutive "1"; ensembl_end_phase "1"; ensembl_phase "-1"; rank "1"; biotype "protein_coding"; transcript_id "AT1G01010.1"; protein_id "AT1G01010.1";
1   araport11   exon    3996    4276    .   +   .   transcript_id "transcript:AT1G01010.1"; gene_id "gene:AT1G01010"; gene_name "NAC001"; Name "AT1G01010.1.exon2"; constitutive "1"; ensembl_end_phase "0"; ensembl_phase "1"; rank "2"; biotype "protein_coding"; transcript_id "AT1G01010.1"; protein_id "AT1G01010.1";
 1 araport11   exon    4706    5095    .   +   .   transcript_id "transcript:AT1G01010.1"; gene_id "gene:AT1G01010"; gene_name "NAC001"; Name "AT1G01010.1.exon4"; constitutive "1"; ensembl_end_phase "0"; ensembl_phase "0"; rank "4"; biotype "protein_coding"; transcript_id "AT1G01010.1"; protein_id "AT1G01010.1";
1   araport11   exon    4706    5095    .   +   .   transcript_id "transcript:AT1G01010.1"; gene_id "gene:AT1G01010"; gene_name "NAC001"; Name "AT1G01010.1.exon4"; constitutive "1"; ensembl_end_phase "0"; ensembl_phase "0"; rank "4"; biotype "protein_coding"; transcript_id "AT1G01010.1"; protein_id "AT1G01010.1";

I have used the featureCounts for counting the alingned SAM files (STAR alignment). Any guidance from you will be very helpful.

Thank you

rna-seq • 104 views
ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by umeshtanwar210

Please follow up to your other thread: C: Differential gene expression DESeq2

ADD REPLYlink written 6 weeks ago by Kevin Blighe41k

Hello umeshtanwar2!

Questions similar to yours can already be found at:

We have closed your question to allow us to keep similar content in the same thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

ADD REPLYlink written 6 weeks ago by ATpoint15k
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