Entering edit mode
5.1 years ago
umeshtanwar2
▴
30
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