Hello friends,
I have executed cuffmerge (cuffmerge -o Output -g Homo_sapiens.GRCh38.95.gtf -p 5 assemblies.txt) but unable to get FPKM values in output file “merged.gtf”.
please let me know the reasons of this issue.
Please help me. Thanks
Vivek
some initial lines of merged.gtf file for:
1 | Cufflinks | exon | 11869 | 12227 | . | + | . | gene_id “XLOC_000001”; transcript_id “TCONS_00000003”; exon_number “1”; gene_name “DDX11L1”; oId “ENST00000456328”; nearest_ref “ENST00000456328”; class_code “=”; tss_id “TSS1”; |
---|---|---|---|---|---|---|---|---|
1 | Cufflinks | exon | 12613 | 12721 | . | + | . | gene_id “XLOC_000001”; transcript_id “TCONS_00000003”; exon_number “2”; gene_name “DDX11L1”; oId “ENST00000456328”; nearest_ref “ENST00000456328”; class_code “=”; tss_id “TSS1”; |
1 | Cufflinks | exon | 13221 | 14409 | . | + | . | gene_id “XLOC_000001”; transcript_id “TCONS_00000003”; exon_number “3”; gene_name “DDX11L1”; oId “ENST00000456328”; nearest_ref “ENST00000456328”; class_code “=”; tss_id “TSS1”; |
1 | Cufflinks | exon | 11869 | 12057 | . | + | . | gene_id “XLOC_000001”; transcript_id “TCONS_00000002”; exon_number “1”; gene_name “DDX11L1”; oId “CUFF.1.3”; nearest_ref “ENST00000450305”; class_code “j”; tss_id “TSS1”; |
1 | Cufflinks | exon | 12179 | 12227 | . | + | . | gene_id “XLOC_000001”; transcript_id “TCONS_00000002”; exon_number “2”; gene_name “DDX11L1”; oId “CUFF.1.3”; nearest_ref “ENST00000450305”; class_code “j”; tss_id “TSS1”; |
1 | Cufflinks | exon | 12613 | 12721 | . | + | . | gene_id “XLOC_000001”; transcript_id “TCONS_00000002”; exon_number “3”; gene_name “DDX11L1”; oId “CUFF.1.3”; nearest_ref “ENST00000450305”; class_code “j”; tss_id “TSS1”; |
1 | Cufflinks | exon | 13221 | 13374 | . | + | . | gene_id “XLOC_000001”; transcript_id “TCONS_00000002”; exon_number “4”; gene_name “DDX11L1”; oId “CUFF.1.3”; nearest_ref “ENST00000450305”; class_code “j”; tss_id “TSS1”; |
1 | Cufflinks | exon | 13453 | 14409 | . | + | . | gene_id “XLOC_000001”; transcript_id “TCONS_00000002”; exon_number “5”; gene_name “DDX11L1”; oId “CUFF.1.3”; nearest_ref “ENST00000450305”; class_code “j”; tss_id “TSS1”; |
1 | Cufflinks | exon | 11869 | 12057 | . | + | . | gene_id “XLOC_000001”; transcript_id “TCONS_00000001”; exon_number “1”; gene_name “DDX11L1”; oId “CUFF.1.2”; nearest_ref “ENST00000450305”; class_code “=”; tss_id “TSS1”; |
1 | Cufflinks | exon | 12179 | 12227 | . | + | . | gene_id “XLOC_000001”; transcript_id “TCONS_00000001”; exon_number “2”; gene_name “DDX11L1”; oId “CUFF.1.2”; nearest_ref “ENST00000450305”; class_code “=”; tss_id “TSS1”; |
1 | Cufflinks | exon | 12613 | 12697 | . | + | . | gene_id “XLOC_000001”; transcript_id “TCONS_00000001”; exon_number “3”; gene_name “DDX11L1”; oId “CUFF.1.2”; nearest_ref “ENST00000450305”; class_code “=”; tss_id “TSS1”; |
1 | Cufflinks | exon | 12975 | 13052 | . | + | . | gene_id “XLOC_000001”; transcript_id “TCONS_00000001”; exon_number “4”; gene_name “DDX11L1”; oId “CUFF.1.2”; nearest_ref “ENST00000450305”; class_code “=”; tss_id “TSS1”; |