Hello,
Can someone help me understanding GTF files generated by stringtie merge. I have downloaded three bam files (repeat) online for a RNA-seq experiment. These bam files were the created by using Tophat. I created GTF file using stringtie with -G option and GTF reference annotation file I downloaded from ensembl. I merged these GTF files (from three bam files) using stringtie --merge with -G option using reference annotation file. The output GTF file has two sources for transcripts; stringtie and ensembl. The transcripts from source ensembl do not even there in original stringtie GTF file that was generated from bam file using Stringtie. Why do we see two sources after merging?
I want to have merged GTF file that has transcripts (novel and known) expressed only in the samples. how will I do that. Any help will be much appreciated.
1 answer
The transcripts marked with an Ensembl source in your output file will have been taken directly from the reference GTF you provided to -G. When you use the -G option, all transcripts from the reference annotation are included in your merged annotation. There is no option I'm aware of in stringtie to filter transcripts from the reference annotation for expression. I far as I'm aware, the filtering options only apply to the transcripts coming from the assemblies you are merging.
Log in to answer this question.
-
Clarification on StringTie's `--merge` parameters
written by DGTool •
-
Multi-fasta file for gffread
written by vitor •
-
StringTie merged transcripts for two different conditions
written by vitor •
-
Question about gffcompare using multiple reference annotations from different databases
written by newbie
-
Transcriptomic assembly Stringtie
written by Nelislam4 •
-
lncRNA Detection with Tuxedo Suite
written by 27atcggcta27
-
Clarification in the workflow steps of the RNA-seq analysis for differential gene analysis
written by amy16 •
-
gffread error when extracting transcript sequences from gtf, coordinates exceed sequence length
written by jjrin •
-
StringTie final sample gtf
written by samuel
-
Error message whengenerating read coverage tables for Ballgown by stringtie
written by hu.guangzhen9 •
I'm not sure what exactly you mean with 'merging' but perhaps you can have a look at the AGAT toolkit AGAT doc . it has functionality to merge GFF/GTF files.
likely you will need to transform you GTF to GFF first
stringtie mergeis part of the stringtie suite, and generates a consensus GTF file by comparing multiple assemblies and merging compatible transcripts.