Question: gffcompare class code 'j'
1
gravatar for waqaskhokhar999
8 months ago by
waqaskhokhar99980 wrote:

I have merged transcriptome assembly of 728 accessions and compare it with Arabidopsis refernce annotation file (ftp://ftp.ensemblgenomes.org/pub/release-43/plants/gtf/arabidopsis_thaliana) using gffcompare. Its stat' output is:

gffcompare -r /media/waqas/second/Analysis/TAIR10_genome/ensemble_gtf/Arabidopsis_thaliana.TAIR10.42.gtf -o gffcompare stringtie_merged.gtf

Summary for dataset: stringtie_merged.gtf

Query mRNAs : 126199 in 32235 loci (112943 multi-exon transcripts)

(17283 multi-transcript loci, ~3.9 transcripts per locus)

Reference mRNAs : 53516 in 32046 loci (42815 multi-exon)

Super-loci w/ reference transcripts: 27093

              | Sensitivity | Precision  |

    Base level:   100.0     |    86.5    |

    Exon level:   100.0     |    66.0    |

  Intron level:   100.0     |    70.0    |

Intron chain level:    99.6     |    37.8    |

Transcript level:    99.6     |    42.2    |

   Locus level:   100.0     |    89.3    |


 Matching intron chains:   42644
   Matching transcripts:   53316
          Matching loci:   32046

      Missed exons:       0/192402  (  0.0%)
       Novel exons:   27127/342721  (  7.9%)
    Missed introns:       1/132525  (  0.0%)
     Novel introns:   22825/189217  ( 12.1%)
       Missed loci:       0/32046   (  0.0%)
        Novel loci:    3349/32235   ( 10.4%)

 Total union super-loci across all input datasets: 32235 
126199 out of 126199 consensus transcripts written in gffcompare.annotated.gtf (0 discarded as redundant)

Besides that It generated five more files, I have checked the literature and found that class code 'j' reflects novel isoforms but the occurrence of j varies in gffcompare output files:

gffcompare.annotated.gtf (count of j: 1000)

gffcompare.stringtie_merged.gtf.tmap (count of j: 2807)

gffcompare.tracking (count of j: 2876)

How can I get the idea of actual number of novel isoforms?

gffcompare rna-seq • 345 views
ADD COMMENTlink modified 8 months ago by genomax76k • written 8 months ago by waqaskhokhar99980

Hi waqaskhokhar999 , I changed the topic tag of your post to 'question' , the 'tool' tag is reserved for advertising new tools and such.

ADD REPLYlink written 8 months ago by lieven.sterck6.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1068 users visited in the last hour