Cummerbund get locus

[nr23]

Hi,

I've mapped PE RNA-Seq reads to a Unigene database, with each scaffold representing an expressed gene, and annotated with the gene information (I don't have an annotation.gtf file).

I've now managed to persuade cufflinks/merge/diff to accept my headers and have the following in my gene_exp.diff (only 1st few columns):

test_id gene_id gene locus

XLOC_000002 XLOC_000002 -
PREDICTEDXenopusSiluranatropicalisFcfragmentofIgGbindingproteinfcgbpmRNA5407:11-406

As you can see, the information I want to access is in the locus field rather than 'gene'. Thus I am unable to pull it out using the getGenes function in cummeRbund.

Anyone got any good tips for how to access this information so that I can annotate plots with it?

I appreciate this is a somewhat strange problem!

Cheers,

N

[jmwhitha]

How did you get your diff_genes.txt file to include locus as a column?