Question: RNA seq: tuxedo protocol - separate non-overlapping genes of same XLOC id in cuffdiff output
1
gravatar for CHANG
3.8 years ago by
CHANG40
United States
CHANG40 wrote:

I notice that there're two non-overlapping genes (PHLDB3, ETHE1) , but they have the same XLOC id = XLOC_018276

# cuffmerge's output - merged.gtf

gene_id "XLOC_018276"; transcript_id "TCONS_00085241"; exon_number "16"; gene_name "PHLDB3"; oId "NM_198850"; nearest_ref "NM_198850"; class_code "="; tss_id "TSS34843"; p_id "P15382";
chr19 Cufflinks
exon 44009900
44009902 .
- .
gene_id "XLOC_018276"; transcript_id "TCONS_00085242"; exon_number "1"; gene_name "ETHE1"; oId "CUFF.30707.12"; nearest_ref "NM_014297"; class_code "j"; tss_id "TSS34842";
chr19 Cufflinks
exon 44010944
44011054 .

Thus, when i run cuffdiff, I get one value of fold change for both genes. 

test_id    gene_id    gene    locus    sample_1    sample_2    status    value_1    value_2    log2(fold_change of value2/value1)    test_stat    p_value    q_value    significant

XLOC_018276    XLOC_018276    ETHE1,PHLDB3    chr19:43978502-44031860    tumor    normal    OK    222.08    450.931    1.02183    1.29159    0.00005    0.00321114    yes     

 

How do I get separate fold changes for ETHE1 and PHLDB3? 

 

rna-seq • 3.5k views
ADD COMMENTlink modified 3.8 years ago • written 3.8 years ago by CHANG40

If you look at your alignments, do you see a lot of reads mapping in between the two genes? Cufflinks will merge them in that case.

ADD REPLYlink written 3.8 years ago by Devon Ryan81k

There are more reads in ETHE1 than PHLDB3 , it doesn't seem like cufflink should merge them. I have attached a screen shot of igv

ADD REPLYlink modified 3.8 years ago by Devon Ryan81k • written 3.8 years ago by CHANG40

N.B., I updated your post so that the image shows.

My guess is that cufflinks sees the reads between the two genes as joining them. They may in fact be transcribed as a unit sometimes, so cufflinks might not be wrong in doing that.

ADD REPLYlink written 3.8 years ago by Devon Ryan81k
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