Empty cuffdiff files

[repinementer]

Dear cufflinks users

I used cuffdiff command on one sample (gtf file) against 10 samples (sam files)
Though I got nice results of gene_exp.diff and isoform_exp.diff and genes.fpkm_tracking and isoform.fpkm_tracking I could n't able to get any kind of results in cds.diff, cds_exp.diff, promoters.diff, splicing.diff and tss_group, exp.diff.

Does any one know wy? Do we need to use any special options to point those?

I just ran the command in the manual

cuffdiff   file.gtf   f1.sam f2.sam f3.sam .......f10.sam

-rw-rw-r-- 1 user user 81 Aug 16 17:40 0_1_cds.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 0_1_cds_exp.diff
-rw-rw-r-- 1 user user 1239587 Aug 16 17:40 0_1_gene_exp.diff
-rw-rw-r-- 1 user user 1269381 Aug 16 17:40 0_1_isoform_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 0_1_promoters.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 0_1_splicing.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 0_1_tss_group_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 1_2_cds.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 1_2_cds_exp.diff
-rw-rw-r-- 1 user user 1244129 Aug 16 17:40 1_2_gene_exp.diff
-rw-rw-r-- 1 user user 1273834 Aug 16 17:40 1_2_isoform_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 1_2_promoters.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 1_2_splicing.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 1_2_tss_group_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 2_3_cds.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 2_3_cds_exp.diff
-rw-rw-r-- 1 user user 1230406 Aug 16 17:40 2_3_gene_exp.diff
-rw-rw-r-- 1 user user 1259932 Aug 16 17:40 2_3_isoform_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 2_3_promoters.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 2_3_splicing.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 2_3_tss_group_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 3_4_cds.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 3_4_cds_exp.diff
-rw-rw-r-- 1 user user 1241031 Aug 16 17:40 3_4_gene_exp.diff
-rw-rw-r-- 1 user user 1270585 Aug 16 17:40 3_4_isoform_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 3_4_promoters.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 3_4_splicing.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 3_4_tss_group_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 4_5_cds.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 4_5_cds_exp.diff
-rw-rw-r-- 1 user user 1220536 Aug 16 17:40 4_5_gene_exp.diff
-rw-rw-r-- 1 user user 1250224 Aug 16 17:40 4_5_isoform_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 4_5_promoters.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 4_5_splicing.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 4_5_tss_group_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 5_6_cds.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 5_6_cds_exp.diff
-rw-rw-r-- 1 user user 1219221 Aug 16 17:40 5_6_gene_exp.diff
-rw-rw-r-- 1 user user 1248906 Aug 16 17:40 5_6_isoform_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 5_6_promoters.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 5_6_splicing.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 5_6_tss_group_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 6_7_cds.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 6_7_cds_exp.diff
-rw-rw-r-- 1 user user 1234666 Aug 16 17:40 6_7_gene_exp.diff
-rw-rw-r-- 1 user user 1264268 Aug 16 17:40 6_7_isoform_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 6_7_promoters.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 6_7_splicing.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 6_7_tss_group_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 7_8_cds.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 7_8_cds_exp.diff
-rw-rw-r-- 1 user user 1240311 Aug 16 17:40 7_8_gene_exp.diff
-rw-rw-r-- 1 user user 1269932 Aug 16 17:40 7_8_isoform_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 7_8_promoters.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 7_8_splicing.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 7_8_tss_group_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 8_9_cds.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 8_9_cds_exp.diff
-rw-rw-r-- 1 user user 1208285 Aug 16 17:40 8_9_gene_exp.diff
-rw-rw-r-- 1 user user 1237988 Aug 16 17:40 8_9_isoform_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 8_9_promoters.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 8_9_splicing.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 8_9_tss_group_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 9_10_cds.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 9_10_cds_exp.diff
-rw-rw-r-- 1 user user 1220632 Aug 16 17:40 9_10_gene_exp.diff
-rw-rw-r-- 1 user user 1250339 Aug 16 17:40 9_10_isoform_exp.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 9_10_promoters.diff
-rw-rw-r-- 1 user user 81 Aug 16 17:40 9_10_splicing.diff
-rw-rw-r-- 1 user user 89 Aug 16 17:40 9_10_tss_group_exp.diff
-rw-rw-r-- 1 user user 2261734908 Aug 11 06:54 accepted_hits.sam
-rw-rw-r-- 1 user user 67 Aug 16 17:40 cds.fpkm_tracking
-rw-rw-r-- 1 user user 327377694 Aug 11 06:56 coverage.wig
-rw-rw-r-- 1 user user 20100437 Aug 15 16:58 genes.expr
-rw-rw-r-- 1 user user 4572834 Aug 16 17:40 genes.fpkm_tracking
-rw-rw-r-- 1 user user 4604190 Aug 16 17:40 isoforms.fpkm_tracking
-rw-rw-r-- 1 user user 17148568 Aug 11 06:47 junctions.bed
drwxrwxr-x 2 user user 4096 Aug 11 06:40 logs
-rw-rw-r-- 1 user user 25367498 Aug 15 16:58 transcripts.expr
-rw-rw-r-- 1 user user 135915768 Aug 15 16:58 transcripts.gtf
-rw-rw-r-- 1 user user 67 Aug 16 17:40 tss_groups.fpkm_tracking

[Balat]

I think you may have to run cuffcompare with gtf file from each of your 10 samples. Then run cuffdiff with stdout.combined.gtf file obtained from cuffcompare. Did you use a reference annotation? According to the manual, you will get cds.diff, cds_exp.diff files only if you use reference annotation.
I am not sure if this will help but am interested to know the results after you run cuffcompare.