Class_Code In Isoform-Fpkm-Tracking

Question

[GPR]

Hello, In the isoform-fpkm-tracking file produced by CuffDiff, I am having trouble, understanding the meaning of class codes, viz,

class_code =, class_code j, class_code x or class_code o

Any help?

Thanks, G.

Answer 1

[Sukhi Singh]

Isn't its the same as of cuffcompare, from the manual

Class Codes

If you ran cuffcompare with the -r option, tracking rows will contain the following values. If you did not use -r, the rows will all contain "-" in their class code column. Priority Code Description

1 = Complete match of intron chain

2 c Contained
3 j Potentially novel isoform (fragment): at least one splice junction is shared with a reference transcript
4 e Single exon transfrag overlapping a reference exon and at least 10 bp of a reference intron, indicating a possible pre-mRNA fragment.
5 i A transfrag falling entirely within a reference intron
6 o Generic exonic overlap with a reference transcript
7 p Possible polymerase run-on fragment (within 2Kbases of a reference transcript)
8 r Repeat. Currently determined by looking at the soft-masked reference sequence and applied to transcripts where at least 50% of the bases are lower case

9 u Unknown, intergenic transcript
10 x Exonic overlap with reference on the opposite strand
11 s An intron of the transfrag overlaps a reference intron on the opposite strand (likely due to read mapping errors)
12 . (.tracking file only, indicates multiple classifications)

Also, class code will be "-" if not a transcript, or if class_code isn't present

[GPR]

This was very helpful, thanks!