Cuffdiff problem output!!!

[ALOK N PATEL]

i have some problem related to cuffidiff output, i used this command for replicates:

cuffdiff -o diff_out -b <genome.fa> -p 10 -L CT,SS --total-hits-norm -u cuffmerge_experiment/merged.gtf tophat_exp/exp1/accepted_hits.bam,tophat_exp1/exp2/accepted_hits.bam tophat_exp/exp3/accepted_hits.bam,tophat_exp/exp4/accepted_hits.bam

in my output file i found gene column is empty:

TCONS_00000001 XLOC_000001 - C11044824:403-1007 CT SS OK 4.25634 4.05292 -0.0706522 0.148488 0.881958 0.999985 no
TCONS_00000002 XLOC_000002 - C11047824:1-1042 CT SS OK 4.96333 5.54938 0.161018 -0.40853 0.682884 0.999985 no
TCONS_00000003 XLOC_000003 - C11048020:0-588 CT SS OK 3.66925 4.25115 0.212368 -0.422853 0.672403 0.999985 no
TCONS_00000004 XLOC_000004 - C11048338:216-588 CT SS OK 0.795992 0.604691 -0.396557 0.258201 0.796252 0.999985 no
TCONS_00000005 XLOC_000005 - C11049822:426-1035 CT SS OK 0.359691 0.790309 1.13566 -0.675737 0.499208 0.999985 no

i cant understand how can be its possible, if any one have suggestion please guide me.

upto cuffmerge i found gene in my file like this:

[CODE]C11111420 Cufflinks exon 726 1304 . - . gene_id "XLOC_000033"; transcript_id "TCONS_00000034"; exon_number "1"; oId "Ca_28192"; nearest_ref "Ca_28192"; class_code "="; tss_id "TSS33"; p_id "P11";
C11112120 Cufflinks exon 391 1218 . + . gene_id "XLOC_000034"; transcript_id "TCONS_00000035"; exon_number "1"; oId "Ca_27742"; nearest_ref "Ca_27742"; class_code "="; tss_id "TSS34"; p_id "P12";
C11112120 Cufflinks exon 1577 1657 . + . gene_id "XLOC_000034"; transcript_id "TCONS_00000035"; exon_number "2"; oId "Ca_27742"; nearest_ref "Ca_27742"; class_code "="; tss_id "TSS34"; p_id "P12";
C11112120 Cufflinks exon 1929 2126 . - . gene_id "XLOC_000035"; transcript_id "TCONS_00000036"; exon_number "1"; oId "Ca_27743"; nearest_ref "Ca_27743"; class_code "="; tss_id "TSS35"; p_id "P13";
C11115550 Cufflinks exon 6 533 . + . gene_id "XLOC_000036"; transcript_id "TCONS_00000037"; exon_number "1"; oId "Ca_27676"; nearest_ref "Ca_27676"; class_code "="; tss_id "TSS36"; p_id "P14";
C11115550 Cufflinks exon 2561 2800 . - . gene_id "XLOC_000037"; transcript_id "TCONS_00000038"; exon_number "1"; oId "Ca_27677"; nearest_ref "Ca_2767

[lindenb]

cross posted on http://www.biostars.org/p/87526

[ALOK N PATEL]

This problem is being faced by my friend he posted it on biostar but he was not able to do the same in seqanswers!!