Cuffcompare : Why is the number of loci different from union of super-loci?
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5.3 years ago

I have a cuffcompare.stats file that contains :

# Cuffcompare v2.2.1 | Command line was:
#cuffcompare -o cuffmerge/cuffcompare -r /reference/mus_musculus/GRCm38/ensembl/release-86/Annotation/Genes/gtf/Mus_musculus.GRCm38.86.gtf -R -s /reference/mus_musculus/GRCm38/ensembl/release-86/Sequence/Chromosomes/ -C -V cuffmerge/merged.gtf
#

#= Summary for dataset: cuffmerge/merged.gtf :
#     Query mRNAs :  151818 in   59836 loci  (114796 multi-exon transcripts)
#            (17978 multi-transcript loci, ~2.5 transcripts per locus)
# Reference mRNAs :  117527 in   47037 loci  (95479 multi-exon)
# Super-loci w/ reference transcripts:    41604
#--------------------|   Sn   |  Sp   |  fSn |  fSp  
        Base level:     100.0    74.3     -       -   
        Exon level:     113.0   110.3   100.0   100.0
      Intron level:      99.6    96.4   100.0    98.7
Intron chain level:      80.0    66.5   100.0   100.0
  Transcript level:      76.6    59.3    72.7    56.2
       Locus level:      99.6    77.3   100.0    77.5

     Matching intron chains:   76386
              Matching loci:   46831

          Missed exons:       2/396144  (  0.0%)
           Novel exons:   18667/405769  (  4.6%)
        Missed introns:     781/261696  (  0.3%)
         Novel introns:    1838/270629  (  0.7%)
           Missed loci:       0/47037   (  0.0%)
            Novel loci:   12834/59836   ( 21.4%)

 Total union super-loci across all input datasets: 59834

where

wc -l cuffmerge/cuffcompare/cuffcompare.loci
> 59834 cuffmerge/cuffcompare/cuffcompare.loc

The last line says that there 59834 "super-loci", however the line above seems to imply 59836 loci. What is the difference?

Likewise when I count the number of loci with novel transcripts (ie class_code = "j"), I get 12627 instead of 12834.

grep "class_code \"j\"" cuffmerge/merged.gtf | awk 'BEGIN{FS="\t"}{print $9}' | awk '{print $2}' | sort | uniq | wc -l
12627

What is the difference here also?

cufflinks cuffcompare • 1.8k views
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