I intend to account for transposable elements in my mapping and quantification process. Specifically, I was hoping for a tool that does quantification at the …

I'm wondering if someone can check my work using STAR to map and StringTie for assembly and quantification. My data is from RNAseq on 29 …

I am trying to use gffcompare to compare my assembled transcriptome to a reference gtf that contains information about small open reading frames (sORFs). The …

Hi I am looking at the Ensembl V100 gtf annotation file for one model animal of interest and found the annotation lacks a number of …

Hi all, I was wondering how to find novel transcripts under different treatment conditions using stringTie? I have 4 different treatments and 3 replications for …

Hi, I am trying to find novel transcripts from an RNA-seq database ([as mentioned in my previous question][1]). Based on the advice I got, it …

I have merged transcriptome assembly of 728 accessions and compare it with Arabidopsis refernce annotation file (ftp://ftp.ensemblgenomes.org/pub/release-43/plants/gtf/arabidopsis_thaliana) using gffcompare. Its stat' output is: gffcompare -r …

Hi Everyone, I am trying to find out all transcripts that are a subfragment of any other transcript from a gtf file. By subfragment, I …

Hello all, So, Im running a test dataset available here https://github.com/Arabinet/Introduction-to-Bioinformatics/wiki/Arabidopsis-RNA-Seq through an RNAseq pipeline I hope to use for experimental data later. I have …

Hi all, Below is the output from gffcompare of assembled transcripts from my RNA-seq experiment with the reference genome annotation. I am concerned about the …