gene ID is missing in Cuffdiff output

Question

[zzygyx9119]

Hi All,

I did RNAseq data analysis using Tophat-Cufflink. One problem I have is that in the "diff_out" file from Cuffdiff, I didn't get the gene_ID (in this case, for example, at1g30220 of Arabidopsis gene ID). I only got the gene name (such as AAC1 shown below). Would you please help me solve this problem? Thanks a lot!

zzy9119

Here is the example of the output I got:

test_id       gene_id       gene          locus
1-Oct         1-Oct         1-Oct         1:27538275-27541944
2-Cys Prx B   2-Cys Prx B   2-Cys Prx B   5:1919212-1921425
2-Oct         2-Oct         2-Oct         1:29854037-29855821
2A6           2A6           2A6           1:844435-847683
3-Oct         3-Oct         3-Oct         1:5602872-5604663
3BETAHSD/D1   3BETAHSD/D1   3BETAHSD/D1   1:17335848-17339273
3BETAHSD/D2   3BETAHSD/D2   3BETAHSD/D2   2:11178099-11182976
4-Oct         4-Oct         4-Oct         3:7225134-7228595
4CL1          4CL1          4CL1          1:19158751-19161552
4CL2          4CL2          4CL2          3:7454268-7457379
4CL3          4CL3          4CL3          1:24167201-24171502
4CL5          4CL5          4CL5          3:7448039-7452000
5-FCL         5-FCL         5-FCL         5:4133203-4138792
5-Oct         5-Oct         5-Oct         1:29867879-29869633
5PTASE11      5PTASE11      5PTASE11      1:17435564-17438396
5PTASE13      5PTASE13      5PTASE13      1:1682317-1687363
5PTASE2       5PTASE2       5PTASE2       4:9991011-9994420
A7            A7            A7            4:14043939-14044902
AAC1          AAC1          AAC1          3:2605441-2607787
AAC2          AAC2          AAC2          5:4335466-4337680
AAC3          AAC3          AAC3          4:14034653-14043278
AACT1         AACT1         AACT1         5:24608723-24610304
AAE1          AAE1          AAE1          1:7119675-7121817
AAE12         AAE12         AAE12         1:24512456-24514659
AAE14         AAE14         AAE14         1:10810983-10813700
AAE15         AAE15         AAE15         4:8111961-8118160
AAE16         AAE16         AAE16         3:8575166-8581112

[GouthamAtla]

Can you paste first few lines from your annotation file i.e GTF or GFF which was used?

[zzygyx9119]

Hi Geek_y,

Thank you for your kind help. Here is the first 15 lines of the .GTF file I used.

1    unknown    exon    3631    3913    .    +    .    gene_id "NAC001"; gene_name "NAC001"; p_id "P20202"; transcript_id "NM_099983.2"; tss_id "TSS18959";
1    unknown    CDS    3760    3913    .    +    0    gene_id "NAC001"; gene_name "NAC001"; p_id "P20202"; transcript_id "NM_099983.2"; tss_id "TSS18959";
1    unknown    start_codon    3760    3762    .    +    .    gene_id "NAC001"; gene_name "NAC001"; p_id "P20202"; transcript_id "NM_099983.2"; tss_id "TSS18959";
1    unknown    CDS    3996    4276    .    +    2    gene_id "NAC001"; gene_name "NAC001"; p_id "P20202"; transcript_id "NM_099983.2"; tss_id "TSS18959";
1    unknown    exon    3996    4276    .    +    .    gene_id "NAC001"; gene_name "NAC001"; p_id "P20202"; transcript_id "NM_099983.2"; tss_id "TSS18959";
1    unknown    CDS    4486    4605    .    +    0    gene_id "NAC001"; gene_name "NAC001"; p_id "P20202"; transcript_id "NM_099983.2"; tss_id "TSS18959";
1    unknown    exon    4486    4605    .    +    .    gene_id "NAC001"; gene_name "NAC001"; p_id "P20202"; transcript_id "NM_099983.2"; tss_id "TSS18959";
1    unknown    CDS    4706    5095    .    +    0    gene_id "NAC001"; gene_name "NAC001"; p_id "P20202"; transcript_id "NM_099983.2"; tss_id "TSS18959";
1    unknown    exon    4706    5095    .    +    .    gene_id "NAC001"; gene_name "NAC001"; p_id "P20202"; transcript_id "NM_099983.2"; tss_id "TSS18959";
1    unknown    CDS    5174    5326    .    +    0    gene_id "NAC001"; gene_name "NAC001"; p_id "P20202"; transcript_id "NM_099983.2"; tss_id "TSS18959";
1    unknown    exon    5174    5326    .    +    .    gene_id "NAC001"; gene_name "NAC001"; p_id "P20202"; transcript_id "NM_099983.2"; tss_id "TSS18959";
1    unknown    CDS    5439    5627    .    +    0    gene_id "NAC001"; gene_name "NAC001"; p_id "P20202"; transcript_id "NM_099983.2"; tss_id "TSS18959";
1    unknown    exon    5439    5899    .    +    .    gene_id "NAC001"; gene_name "NAC001"; p_id "P20202"; transcript_id "NM_099983.2"; tss_id "TSS18959";
1    unknown    stop_codon    5628    5630    .    +    .    gene_id "NAC001"; gene_name "NAC001"; p_id "P20202"; transcript_id "NM_099983.2"; tss_id "TSS18959";
1    unknown    exon    5928    6263    .    -    .    gene_id "ARV1"; gene_name "ARV1"; p_id "P9646"; transcript_id "NM_099984.5"; tss_id "TSS12097";