The cuffcompare command is [1]. There are many gtf files in the gtf.list. I checked one line in tracking file [2]. As shown, the class code is u. It mean that this transcript TCONS_00000010 does not exist in the reference gtf file. This gene's structure was extracted from cuffcompare output combined.gtf [3]. Also the gene information of the scaffold C158694440 on ref.gtf was extracted [4]. As it shown, the position exactly same to the combined.gtf. With these evidence, why dose cuffcompare report this transcript in tracking file as u class code?

[1]

cuffcompare  -i gtf.list  -r ref.gtf  -V -C -G -o output

[2]

TCONS_00000010  XLOC_000010     -       u       -       -       -       -       -       -       -       -       -       -       -    q77:CUFF.34750|CUFF.34750.1|100|14499.423414|5137.328275|23861.518552|36842.740619|-     -       -       -       -       -       -    -

[3]

C158694440      Cufflinks       exon    1       103     .       .       .       gene_id "XLOC_000010"; transcript_id "TCONS_00000010"; exon_number "1"; oId "CUFF.34750.1"; class_code "u"; tss_id "TSS10";

[4]

C158694440      Cufflinks       exon    1       103     .       .       .       gene_id "XLOC_000010"; transcript_id "TCONS_00000010"; exon_number "1"; oId "TCONS_00000010"; class_code "u"; tss_id "TSS10";