Hello.

Im working with cnRNA sequence.fa by ensembl for looking only DE ncRNA. I make all process with tophat-cufflink and cuffdiff. (and after with deseq) ...

So, I have mapping with tophat, and it is ok! When I did cufflink, some genes appear like new transcipts..

ENSSSCT00000026972.1 Cufflinks exon 11 145 . . . gene_id "XLOC_021714"; transcript_id "TCONS_00026884"; exon_number "1"; oId "CUFF.1067.1"; class_code "u"; tss_id "TSS23414";

After cuffdiff:

test_id gene_id gene locus sample_1 sample_2 status value_1 value_2 log2(fold_change) test_stat p_value q_value significant XLOC_021685 XLOC_021685 - ENSSSCT00000021151.1:5-326 q1 q2 OK 61005.1 3982.52 -3.93718 -1.53835 0.0001 0.00655 yes

I tried DE with deseq, considering gtf by ensembl.. any transcripts were found. And when I made with gtf by cuffmerge.. the same transcripts of cufflinks were found.

However, I cant understand some points:

1) any gene name appear for genes with expression. Only a transcrips id in the locus columm. (ps: the locus position is different in ensembl). Why? I can considered this information?

2) However, these DE transcrips there are a gene ID related. When I look for these genes in cuffdiff output, any expression is found. Why these transcripts appear only in locus information and not in gene ?

Thanks in advance.