Gene information in Cuffdiff output files

[hong_sunwoo]

Hello.
I am now trying RNA-seq data analysis using Tophat-Cufflinks process.
I have two human RNA-seq data from Solexa sequencing (single-end) and my goal is comparing gene expression level and alternative splicing patterns of each data.

Without any option, I ran tophat with UCSC hg19 and obtained two accepted_hits.sam files.
Then, through cufflinks and cuffcompare, single gtf file, stdout.combined.gtf file is made and used for cuffdiff along with two sam files.

After cuffdiff run, I could see several files such as gene_exp.diff.

My question is below.
When I open the cuffdiff results files, I can not find gene information as below.

test_id    gene    locus    sample_1    sample_2    status    value_1    value_2    ln(fold_change)    test_stat    p_value    significant
XLOC_000001    -    chr1:763004-764484    q1    q2    NOTEST    0    9.91482    2.13631e-314    1.79769e+308    0    no
XLOC_000002    -    chr1:895380-897112    q1    q2    NOTEST    6.56765    2.24444    -1.0737    1.38868    0.16493    no
XLOC_000003    -    chr1:897214-901465    q1    q2    NOTEST    11.9247    2.23374    -1.67493    4.67081    3.00007e-06    no
XLOC_000004    -    chr1:908878-909553    q1    q2    NOTEST    0    4.13402    2.14785e-314    1.79769e+308    0    no

How can I get gene information?

[Cole Trapnell]

Hello.
I am now trying RNA-seq data analysis using Tophat-Cufflinks process.
I have two human RNA-seq data from Solexa sequencing (single-end) and my goal is comparing gene expression level and alternative splicing patterns of each data.

Without any option, I ran tophat with UCSC hg19 and obtained two accepted_hits.sam files.
Then, through cufflinks and cuffcompare, single gtf file, stdout.combined.gtf file is made and used for cuffdiff along with two sam files.

After cuffdiff run, I could see several files such as gene_exp.diff.

My question is below.
When I open the cuffdiff results files, I can not find gene information as below.

test_id    gene    locus    sample_1    sample_2    status    value_1    value_2    ln(fold_change)    test_stat    p_value    significant
XLOC_000001    -    chr1:763004-764484    q1    q2    NOTEST    0    9.91482    2.13631e-314    1.79769e+308    0    no
XLOC_000002    -    chr1:895380-897112    q1    q2    NOTEST    6.56765    2.24444    -1.0737    1.38868    0.16493    no
XLOC_000003    -    chr1:897214-901465    q1    q2    NOTEST    11.9247    2.23374    -1.67493    4.67081    3.00007e-06    no
XLOC_000004    -    chr1:908878-909553    q1    q2    NOTEST    0    4.13402    2.14785e-314    1.79769e+308    0    no

How can I get gene information?

That field is for the "gene_name" attribute for each transcript. Your GTF file needs to have the "gene_name" attribute attached to it in order to anything to show up there. Ensembl and other annotation sources attach these to their GTF records, and Cuffcompare tries to preserve them in its *.combined.gtf files.

[hong_sunwoo]

Thanks Cole.
I will try cuffcompare using annotation file from Ensemble!