Questions tagged [stringtie]

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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 ...
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18 views

Detecting Transcript Isoforms with HISAT2/Stringtie RNAseq Output

I have the following Stringtie RNA-seq output files for several samples in the image below. For additional context, I have utilized as part of my RNA-seq workflow. HISAT2, samtools, and Stringtie ...
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10 views

Does “Wrapping up the results” in ballgown means that ballgown object is created correctly?

I am trying to apply a Pertea et al. procedure to my RNASeq samples for which I have created a ballgown folder as explained in the article. When I am trying to prepare my phenodata file for every ...
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80 views

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 ...
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128 views

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...
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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 ...