How to get gff annotations and denovo annotations with differential expression result in cuffdiff output

Question

[julianasrinjuli]

Hello Biostars community, I have done differential expression analysis of my RNA-seq data. In my analysis I have used Bowtie2 for alignment and cufflinks and cuffdiff for differential expression analysis. I got result with fold change value. In my reference genome there was annotations for protein product, I post a small portions of my reference gff file ..

AWUE01024918.1  Genbank CDS 28489   28880   .   -   0   ID=cds35702;Parent=rna37279;Dbxref=InterPro:IPR001077,NCBI_GP:OMO49312.1;Name=OMO49312.1;gbkey=CDS;product=O-methyltransferase%2C family 2;protein_id=OMO49312.1
AWUE01024918.1 Genbank CDS 28073 28383 . - 1 ID=cds35702;Parent=rna37279;Dbxref=InterPro:IPR001077,NCBI_GP:OMO49312.1;Name=OMO49312.1;gbkey=CDS;product=O-methyltransferase%2C family 2;protein_id=OMO49312.1

my cufflink result is like that...

AWUE01000013.1  Cufflinks   transcript  1933    3287    1   +   0   gene_id "gene1"; transcript_id "rna1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; full_read_support "no";
AWUE01000013.1 Cufflinks exon 1933 2136 1 + 0 gene_id "gene1"; transcript_id "rna1"; exon_number "1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000"; AWUE01000013.1 Cufflinks exon 2230 2480 1 + 0 gene_id "gene1"; transcript_id "rna1"; exon_number "2"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "0.000000";

and my cuffmerge result is like that ...

AWUE01022029.1  Cufflinks   exon    24589   24666   0   +   0   gene_id "XLOC_037147"; transcript_id "TCONS_00038639"; exon_number "8"; gene_name "COLO4_34006"; oId "rna32701"; nearest_ref "rna32701"; class_code "="; tss_id "TSS37920"; p_id "P31270";
AWUE01022029.1 Cufflinks exon 25033 25145 0 + 0 gene_id "XLOC_037147"; transcript_id "TCONS_00038639"; exon_number "9"; gene_name "COLO4_34006"; oId "rna32701"; nearest_ref "rna32701"; class_code "="; tss_id "TSS37920"; p_id "P31270";

And finally my cuffdiff result is..

XLOC_000001 XLOC_000001 COLO4_00001 AWUE01000002.1:782-1398 O4_0d   O4_3d   NOTEST  0   0   0   0   1   1   no
XLOC_000002 XLOC_000002 COLO4_00002 AWUE01000013.1:1932-3287 O4_0d O4_3d NOTEST 0 0 0 0 1 1 no

what I am missing?? How to get those gff annotations with my cuffdiff result?? how to get protein product name, id, interpro id etc for my result??

Answer 1

[julianasrinjuli]

please help, what can I do. How can I go for further analysis. I am very new to RNA-seq.