how to find novel genes and transcripts in gffcompare?
0
3
Entering edit mode
3.9 years ago

Hello guys, I am new to RNA-SEQ data analysis. I am following the protocol submitted in nature (https://www.nature.com/articles/nprot.2016.095]). I was completed those steps given in the protocol, but i didn't get the novel genes and novel transcripts for my samples. i was running the following command

 gffcompare –r chrX_data/genes/chrX.gtf –G –o merged stringtie_merged.gtf

and i got the result file as

#= Summary for dataset: stringtie_merged.gtf 
#     Query mRNAs :  253181 in   70635 loci  (216728 multi-exon transcripts)
#            (23264 multi-transcript loci, ~3.6 transcripts per locus)
# Reference mRNAs :  216257 in   60158 loci  (189357 multi-exon)
# Super-loci w/ reference transcripts:    51791
#-----------------| Sensitivity | Precision  |
        Base level:   100.0     |    93.0    |
        Exon level:    99.9     |    93.6    |
      Intron level:    99.4     |    94.0    |
Intron chain level:    99.7     |    87.1    |
  Transcript level:    99.8     |    85.2    |
       Locus level:   100.0     |    84.4    |

     Matching intron chains:  188838
       Matching transcripts:  215729
              Matching loci:   60158

          Missed exons:       0/623537  (  0.0%)
           Novel exons:   23741/674273  (  3.5%)
        Missed introns:    2160/383827  (  0.6%)
         Novel introns:    4747/405880  (  1.2%)
           Missed loci:       0/60158   (  0.0%)
           Novel loci:   10239/70635    ( 14.5%)

 Total union super-loci across all input datasets: 70632 
253181 out of 253181 consensus transcripts written in merged.annotated.gtf (0 discarded as redundant)

from this .stats file , where i can find the novel genes and transcripts?

RNA-Seq stringtie gffcompare • 4.3k views
ADD COMMENT
0
Entering edit mode

there will be 6 files generated after this step. GTF LOCI STATS REFMAP TMAP TRACKING

what u have given is a stat file content. go through the TMAP file carefully and there will be one column with class codes, which describes the assembled transcripts compare to reference annotation.

ADD REPLY

Login before adding your answer.

Traffic: 2027 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6