Multiple locus id in Cuffdiff output

[anikng]

This is an RNASeq based doubt and if anyone has experieneced similar problem, kindly suggest the solution.

I used Tophat and cufflinks pipeline (as explained in the paper Trapnell et al., 2012) to analyse RANSeq reads from rice samples (control and two treatments). I used 2 replicates or each sample.

Finally, when I check the Cuffdiff result (specifically, the gene_exp.diff file), I get redundant locus_id with different FPKM value. In this forum, i saw the solution for that. Importaltly, in many cases, multiple locus_ids are listed in place of a single id.

For clarity, I am giving a few lines of gne_exp.diff file.


Thanks


gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant
XLOC_000001 LOC_Os01g01010,LOC_Os01g01019,LOC_Os01g01030,LOC_Os01g01040 Chr1:1894-20323 ctrl e19 OK 16.532 15.9978 -0.0473893 -0.218699 0.75605 0.901896 no
XLOC_000002 LOC_Os01g01050,LOC_Os01g01060 Chr1:21825-28651 ctrl e19 OK 20.4096 21.7579 0.0922973 0.419462 0.54785 0.777761 no

[sdriscoll]

I'm not sure what part of the output you posted is redundant.

[anikng]

Hi sdriscoll,

I face two problem when i analyzed the gene_exp.diff file generated by cuffdiff.

1. As mentioned in the previous post, multiple gene id is assigned for a single row of fpkm value. In the example above, LOC_Os01g01019,LOC_Os01g01030,LOC_Os01g01040 are assigned for a rwa of data.

2. Some rows are redundant. I mean same gene id with different fpkm value as below,

XLOC_000044 LOC_Os01g01870 Chr1:477176-481166 ctrl e19 OK 11.6968 19.5005 0.737399 5.00E-05 0.000484157
XLOC_000045 LOC_Os01g01870 Chr1:477176-481166 ctrl e19 OK 0.149605 0.519128 1.79493 0.2667 0.518088

Thanks

[sdriscoll]

The first is what cufflinks/cuffdiff does when there are mulitple isoforms sharing a single gene locus. My interpretation is that the several LOC* names are all isoforms of a single gene.

The second is odd. The only thing I can think of is that the issue is in your annotation and not with cufflinks/cuffdiff.