how to change XLOC ID to Ensembl ID from Cuffdiff

[super0925]

When I did RNA-Seq analysis, the GTF file I used was from Ensembl. The output of cuffdiff replaced the Ensembl IDs with XLOC's although it also output gene names (e.g. MX2). Ensembl IDs were no longer there.
Is there anyway to convert XLOC back to Ensemble IDs, or simply keep the ensembl IDs from my GTF file? how do you guys go about this?
Interesting enough, if I don't run new gene discovery (i.e. without doing cuffmerge step), I got to keep Ensembl IDs.

[Seq-Rue]

Hi super0925,

I ran into the same problem, and realized the merged.gtf file produced by cuffmerge did not use the Ensembl ID as the transcript ID (shown below). Also, in the downstream analysis with cuffdiff, the "oId" ensembl ID is not carried over into the SQLite database.

1 Cufflinks exon 11869 12227 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "1"; gene_name "DDX11L1"; oId "ENST00000456328"; nearest_ref "ENST00000456328"; class_code "="; tss_id "TSS1";
1 Cufflinks exon 12613 12721 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "2"; gene_name "DDX11L1"; oId "ENST00000456328"; nearest_ref "ENST00000456328"; class_code "="; tss_id "TSS1";
1 Cufflinks exon 13221 14409 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000002"; exon_number "3"; gene_name "DDX11L1"; oId "ENST00000456328"; nearest_ref "ENST00000456328"; class_code "="; tss_id "TSS1";

I ended up writing a python script to substitute the 'transcript_id' with the 'oId' in order to maintain the ensembl IDs (below). I used the new merged.gtf file for cuffdiff and that solved my problem.

#!/usr/bin/python

gtf_handle = "/PATH/TO/merged.gtf"
fh = open(gtf_handle, "r")

import re

trans_ids = {}

with open('merged2.gtf', 'w') as f:

for line in fh:
line = line.strip('\n') ##strip the line to remove white spaces
##print line
cuffID = re.findall(r'gene_id \"([\w\.]+)"', line) ##use RE to get lists of cuffid, ensemblId etc
cuffTx = re.findall(r'transcript_id \"([\w\.]+)"', line)
ensemblTx = re.findall(r'oId \"([\w\.]+)"', line)
geneName = re.findall(r'gene_name \"([\w\.]+)"', line)
##print cuffTx[0]
line = str(line).replace(cuffTx[0], ensemblTx[0]) ##unlist the transcript identifiers and replace cufflinksID with ensemblIDs
print line
f.write("%s\n" % str(line)) ##write file out to a .gtf file

1 Cufflinks exon 11869 12227 . + . gene_id "XLOC_000001"; transcript_id "ENST00000456328"; exon_number "1"; gene_name "DDX11L1"; oId "ENST00000456328"; nearest_ref "ENST00000456328"; class_code "="; tss_id "TSS1";
1 Cufflinks exon 12613 12721 . + . gene_id "XLOC_000001"; transcript_id "ENST00000456328"; exon_number "2"; gene_name "DDX11L1"; oId "ENST00000456328"; nearest_ref "ENST00000456328"; class_code "="; tss_id "TSS1";
1 Cufflinks exon 13221 14409 . + . gene_id "XLOC_000001"; transcript_id "ENST00000456328"; exon_number "3"; gene_name "DDX11L1"; oId "ENST00000456328"; nearest_ref "ENST00000456328"; class_code "="; tss_id "TSS1";

Thanks