Entering edit mode
9.0 years ago
pengchy
▴
450
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";