技巧 | 统计 cuffcompare class code

$ 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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