Question: which file used for GO
0
gravatar for fatimarasool135
15 months ago by
fatimarasool13560 wrote:

I have created the following output files by using the stringtie tool 1) Output GTF file containing the assembled transcripts by stringtie

2) A merged GTF file from all sample GTF

I am not sure which of the above file is used further for Gene Ontology by using tool DAVID or agriGO. The output of my file is as:-

Gene ID     Gene Name   Reference   Strand  Start   End     Coverage    FPKM        TPM
  NM_000451   SHOX        chrX        +       624344  646823  0.000000    0.000000    0.000000
  NM_006883   SHOX        chrX        +       624344  659411  0.000000    0.000000    0.000000
  ...

Am I supposed to pick the gene Id and expression value to find gene ontology results. Or there is something else I need to do.

rna-seq R • 374 views
ADD COMMENTlink written 15 months ago by fatimarasool13560

You need to perform differential transcript or differential gene expression to then potentially see if there are over-represented gene ontology terms or whatever your goal is. There is somewhat of a guide here http://ccb.jhu.edu/software/stringtie/index.shtml?t=manual#de if you want to use the developers' of StringTie tool called Ballgown.

ADD REPLYlink modified 15 months ago • written 15 months ago by jean.elbers1.4k

Hi Jean elbers I did differential gene expression by hisat ,string-tie and ballgown. next, i have to do GO ,Singular Enrichment Analysis and KEGG. by using the tool agriGo.I do not know which gene list I have to provide as input to this agriGo tool.

ADD REPLYlink written 15 months ago by fatimarasool13560

list of genes is as

enter code here

feature id fc pval qval gene MSTRG.28632 0.341220148 1.95E-05 0.176761218 gene MSTRG.3615 5.155727198 2.21E-05 0.176761218 gene MSTRG.7507 0.251906716 2.22E-05 0.176761218

I have to use the database AgriGO....According to this tool, gene ids should be in format GenBank ID: AAP50233.1 DDBJ ID: BAB11514.1 EMBL ID: CAA18188.1 UniProt ID: Q9LYA9 RefSeq Peptide ID: NP_564434 PDB ID: 2zsi_B Wheat Affymetrix Genome Array: Ta.10183.2.S1_at but as you have seen mine data set gene list contain different gene ids ,how can I chang it

ADD REPLYlink modified 15 months ago • written 15 months ago by fatimarasool13560
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