Cuffmerge drops gene_ids and transcript features?

[mary12]

Hello All,

I have run cufflinks on 6 different samples. I want to use cuffmerge to combine the .gtf files for cuffdiff. However, I have two problems.

ex. ind.gtf:
GL349621.1 Cufflinks transcript 163188 166581 1000 - . gene_id "ACYPI52640"; transcript_id "ACYPI52640-RA"; FPKM "16.6471765920"; frac "0.641012"; conf_lo "15.699389"; conf_hi "17.594964"; cov "133.457105"; full_read_support "yes";
GL349621.1 Cufflinks exon 163188 164381 1000 - . gene_id "ACYPI52640"; transcript_id "ACYPI52640-RA"; exon_number "1"; FPKM "16.6471765920"; frac "0.641012"; conf_lo "15.699389"; conf_hi "17.594964"; cov "133.457105";


merged.gtf:
GL349621.1 Cufflinks exon 159336 159819 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "1"; oId "CUFF.3.1"; tss_id "TSS1";
GL349621.1 Cufflinks exon 159902 160013 . + . gene_id "XLOC_000001"; transcript_id "TCONS_00000001"; exon_number "2"; oId "CUFF.3.1"; tss_id "TSS1";


1) In the third column of the ind.gtf files there are exons and transcript. When I run cuffmerge the transcript lines are not there? Only exon features are left.

2) In the ind. gtf files I have gene_ids, but when my files are merged cuffmerge seems to remove the gene_id's and replace them with the XLOC numbers. Is there any way to prevent this from happening?