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
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
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