gffcompare
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gpertea
classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF
I used stringtie ballgown pipeline for my data analysis. I am trying to categorize my differentially expressed transcript in novel and known using gffcomapre. During categorization, I found some MSTRGs...
I always has one doubt for the code "=", if the query is an exact match of intron chain, but the last exon is longer than the reference, why is...
Hi, Which genome browser do you recommend to view the gff file from gffcompare and show cov, FPKM, and TPM in the tracks visually, indicating larger or smaller numbers for...
Hi! I am using GFFCompare and I am providing it with a list of GTF annotation files (without a reference annotation). My goal is to get information from the ".tracking"...
Hi gpertea! I am running GFFCompare by providing it with a list of GTF files. For some transcripts of a specific annotation file, GFFCompare returns this warning: "Warning: merging adjacent/overlapping...
Hi, I have two different gtf files (one created from short reads and the other from long reads), and I would like to compare them to see if any of...
Hi, If I run gffcompare `0.12.6` on an input list of 12 gff3 files my .stats file looks like this (i.e. no sensitivity/precision results): ``` # gffcompare v0.12.6 | Command...
Currently only the basic exon structure and some basic GTF tags are preserved when gffcompare is running in "annotation mode", where a single input transcript file is given (+ a...
Hi, I'm using gffcompare to generate a combined transcripts file from multiple resources. I'm wondering whether we could keep the CDS entry from each resource in the combined.gtf file? It's...
Hi, First, thanks for this utility, it's really useful for my project! I assembled my transcriptome with Stringtie, and this resulted in predicted transcripts that GFFcompare identifies as relating to...
