• Are Novel Junctions Only Give Novel Transcripts?

    In a well annotated GTF/GFF file, The genomic coordinates of exons of genes are present. A gene c...

  • gffcompare class code 'j'

    I have merged transcriptome assembly of 728 accessions and compare it with Arabidopsis refernce a...

  • cuffcompare: No novel genes found. Is this possible?

    I tried to run cuffcompare using cufflink assembled transcript output and an annotation file. I w...

  • Finding Novel Splicing Events/Transcripts Using Tophat And Cufflinks

    Hi There,

    I would like to identify novel splicing events occurring in 4 human paired-end RNA-seq...

  • Cuffmerge potential error

    Hi All,
    so apparently, I have a problem with running tuxedo protocol. 

    Now I have run tophat on ...

  • Validate Novel Isoforms Generated By Cuffcompare

    When I compare the assembled transcripts with a reference annotation with cuffcompare, one of the...

  • error in compare.py of CNCI package

    Hi,

    I am currently working on lncRNA using CNCI package. I have identified more than 10,000 coor...

  • Cufflinks vs. Cuffcompare - number of assembled transcripts

    Hi all,

    I'm having some difficulties in understanding how cufflinks and cuffcompare count the as...

  • Cuffcompare : Why is the number of loci different from union of super-loci?

    I have a cuffcompare.stats file that contains :

    # Cuffcompare v2.2.1 | Command line was:
    ...

  • how to find novel genes and transcripts in gffcompare?

    Hello guys,
    I am new to RNA-SEQ data analysis. I am following the protocol submitt...

  • Selecting and de-selecting exon-exon junctions based on depth or coverage from RNA-seq mapping

    In RNA-seq mapping with TopHat, the exon-exon junctions are reported in junction.bed file. This i...

  • Exons, Strands and Junctions

    Hello!

    I'm getting started in the field of bioinformatics and I'm developing a tool to analyze a...

  • How do you find novel transcripts using GFFcompare?

    Hi, I am trying to find novel transcripts from an RNA-seq database ([as mentioned in my previous ...



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