Questions tagged [stringtie]

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StringTie discovers less novel isoforms when reference annotation is provided

I am analyzing PacBio IsoSeq data and I am using StringTie to assemble transcripts. I noticed the difference in the output files when I add a reference genome annotation (-G option in StringTie). In ...
Aleksandra Greshnova's user avatar
2 votes
0 answers

Why does gene abundance table from StringTie output the same gene ID twice?

I would like to compare gene level counts (FPKM) from StringTie output. I understand FPKM is outdated but my PI prefers to use it as a reference/guide in conjunction with the normalised counts from ...
nattzy's user avatar
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1 vote
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Stringtie/ gene/transcript IDs are wrongly formatted

Hi my RNAseq workflow is ending up with wrongly formatted gene IDs (and separately transcript _IDs) after a Hisat2 ->samtools sort -> stringtie -> workflow. outputs a ...
RichardBJ's user avatar
  • 111
3 votes
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Genome-guided transcriptome reconstruction: should I filter my reference annotation by transcript_support_level or other tags?

Is there really any advantage to filtering the GTF annotation for transcriptome reconstruction (or, for example, for pseudo-alignment quantification)? Are there any downsides (i.e. reasons why I ...
bepoli's user avatar
  • 175
1 vote
1 answer

Assembling all transcripts for an individual gene? (using single sequence to seed the assembly)

Let's say I have a candidate gene and I believe that in an individual sample, the genome sequence differs from the reference which then interferes with alignment. Is there a way for me to do a "...
story's user avatar
  • 1,563
0 votes
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Required input files for StringTie2

I am working on a virtual project for WGS combined with RNA seq for annotation. The RNA will be sequenced using PacBio Isoseq (Sequel II, HiFi-reads). With some research, I found that StringTie2 is ...
WilGos's user avatar
  • 1
2 votes
1 answer

Why this ballgown error (first column of pData does not match the names of the folders) comes out

I am trying to create a ballgown object, and I would like to set a phenodata information. For that I do phenodata <- read.csv('l002.csv') and my l002.csv ...
Dmitrii Trubetskoy's user avatar
2 votes
2 answers

Extract mapping coverage from GTF files

I am doing paired end RNA-seq analysis. I used STAR mapper and then StringTie for getting quantification of my data. After successfully running StringTie, I got .gtf...
Dexter's user avatar
  • 121
1 vote
0 answers

Does StringTie use exon length for gene abundance or complete gene length?

I'm currently using StringTie with option -A for calculating gene abundance (I'm interested in TPM). While checking the manual, I couldn't find any reference to the ...
Siddharth's user avatar
  • 335