Cufflink ID convert

[liuyic]

Hi

I have a question related to Cufflink output file gene.expr.
Any idea how could transfer cufflink gene ID to some commonly used ID (e.g. Gene symbol)?

Best,

[Jon_Keats]

Use a GTF file during the cufflinks process or cuffcompare

Cufflinks
-G/--GTF <reference_annotation.gtf> Tells Cufflinks to use the supplied reference annotation to estimate isoform expression. It will not assemble novel transcripts, and the program will ignore alignments not structurally compatible with any reference transcript.

Cuffcompare
-r An optional "reference" annotation GTF. Each sample is matched against this file, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. See the refmap and tmap output file descriptions below.