$ cut -f4 cuffcompare.tracking | sort | uniq -c
35 =
152 c
37 e
4 i
2 j
11 o
28 p
94 u
9 x
关于 Cufflinks class code 的解释：
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)
Ref | cuffcompare class codes
“识不足则多虑，威不足则多怒，信不足则多言。”
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