stringtie
stringtie copied to clipboard
gpertea
Transcript assembly and quantification for RNA-Seq
When quantified with stringtie, multiple lines were output from a gene. By looking at the gtf file, I found that these were different transcripts of the gene. How do I...
Very appreciative that you developed such good tools. I want to set parameters to ignore strand information using strand-specific RNA-seq in stringtie. How can I set these parameters? Looking forward...
Hello, I have encountered an issue with StringTie's quantification results that vary based on the use of the `-e` option. Specifically, I have observed a difference in the abundance file...
Hi, I have done assemblies using StringTie long, short and mixed options. One isoform that I have seen using short assembly is not showing up when I used mix option....
The aim is to be able to obtain the full transcript sequence in case of unannotated intron retention events. Following the StringTie workflow, this would mean considering retained introns (which...
Hi The official dog gtf annotation on Ensembl V100 is missing some important genes. Interestingly, Ensembl also holds two other dog annotations, based on 2 different breeds. I would like...
1. I have a bunch of Nanopore long-read fastq files that I need to assembly using stringtie. I converted them to bam files using minimap2 and samtools: here is what...
I am running into a similar issue to other users where areas with plenty of RNAseq coverage in IGV are not being properly included in the assembly, even when I...
Hello, I'm trying to find novel transcripts so I don't use the -e option. Using the verbose option, I see in the output that it says `[10/07 16:20:42]^bundle NC_001538:1-5153 done...
Hello, I am using Stringtie in conjunction with CIRIquant and am using the prepDE.py script to generate the gene count matrix for normalization. This has worked with no issue for...
