Cuffdiff isoform_exp.diff output: How do you find which isoform TCONS id is referring to?
0
0
Entering edit mode
5.9 years ago
Yuka Takemon ▴ 40

Hello!

I am analysing RNAseq data using cufflinks/2.2.1 to run cuffdiff for two groups of samples WT vs KO. I am interested in knowing which of the isoforms of a corresponding gene is differentially expressed.

test_id gene_id gene    locus   sample_1    sample_2    status  value_1 value_2 log2(fold_change)   test_stat   p_value q_value significant
TCONS_00005883  XLOC_003696 Myo1c   chr11:75651508-75674634 WT  KO  OK  0.695384    0.813635    0.226571    0.134985    0.7983  0.999954    no
TCONS_00005884  XLOC_003696 Myo1c   chr11:75651508-75674634 WT  KO  OK  2.70472 5.00692 0.888442    2.3638  0.0006  0.327444    no
TCONS_00005885  XLOC_003696 Myo1c   chr11:75651508-75674634 WT  KO  OK  65.5926 118.552 0.853912    3.30047 5.00E-05    0.0508103   no

I know that I should be looking at the TCONS id number, but which transcript is it actually referring to in relation to databases such as Ensembl? and how do can I look this up? In the above example for Myo1c, when you look this gene up on Ensembl there are 5 protein coding transcirpts, but there are only 3 in the cuffdiff output with different id systems.

I would appreciate your input.

Thank you,

Y

RNA-Seq cufflinks cuffdiff transcript_id TCONS • 3.3k views
ADD COMMENT
0
Entering edit mode

If you followed the Tuxedo pipeline, then I'd guess these are in the output from cuffmerge (e.g. merged.gtf). Some sample lines below:

chr1    Cufflinks       exon    788859  794826  .       +       .       gene_id "XLOC_000006"; transcript_id "TCONS_00000013"; exon_number "7"; gene_name "LINC01128"; oId "NR_047520"; nearest_ref "NR_047520"; class_code "="; tss_id "TSS6";
chr1    Cufflinks       exon    762971  763155  .       +       .       gene_id "XLOC_000006"; transcript_id "TCONS_00000015"; exon_number "1"; gene_name "LINC01128"; oId "NR_047522"; nearest_ref "NR_047522"; class_code "="; tss_id "TSS6";
ADD REPLY

Login before adding your answer.

Traffic: 1815 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6