Questions tagged [stringtie]
The stringtie tag has no usage guidance.
9
questions
2
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answer
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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 ...
2
votes
0
answers
121
views
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 I understand FPKM is outdated but my PI prefers to use it as a reference/guide in conjunction with the normalised counts from ...
- 31
1
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0
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109
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Stringtie/DEprep.py 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 -> DEprep.py workflow.
DEprep.py outputs a ...
- 111
3
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23
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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 ...
- 175
1
vote
1
answer
62
views
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 "...
- 1,563
0
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0
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88
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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 ...
- 1
2
votes
1
answer
247
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 ...
2
votes
2
answers
282
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...
- 121
1
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0
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43
views
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 ...
- 335