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• converting .gff file to .gtf
  I am trying to upload annotation file to the galaxy rna seq work flow, but i have annotation in t...
• How to create a gtf using the GRC38 gtf and ERCC92.gtf
  Hi, I am trying to incorporate ERCC spike-ins into my RNA seq experiments. Everything I have rea...
• Assembly database choice for RNA-seq and ChIP-seq
  Hello, First, just a brief mention that this is indeed a topic that has been brought-up in the p...
• RNA-seq- Alternative spliceforms
  Hello, I am interested in identifying alternative splice forms from my RNA-seq data ( mutant and...
• Rna-Seq Analysis With Bacteria, Rrna Reduced, Strand Specific
  I do mostly eukaryotic RNA-seq using Tophat2 and then cufflinks, DEseq, edgeR, etc. I have some ...
• transcript count after string tie merge
  Hi, I am trying to get transcript counts with stringtie merge command. I have set of gtf output, ...
• genes in gtf do not exist in the merged.gtf after cuffmerge
  I use cufflinks pipeline to perform RNA Seq. I have some genes in gtf but after I perform cuffmer...
• Rna Seq Data Analysis
  Hi all!!! I am new to analysis the RNA-seq data. As far now i used bowtie for indexing the refe...
• Which GTF file to use while detecting known and novel non coding RNA
  I am interested in detecting known as well as novel long non coding RNA in mice RNA-Seq samples. ...
• Difference between GTF file with CHR and without CHR. ENSEMBL
  I am very new to RNA-Seq. I am trying to align my samples with STAR. I am generating the genome i...
• rna seq analysis
  Hi, I have gencode long non coding(lnc) gtf and lnc reference fasta files.. if i run tophat u...
• Is It Possible To Get Features Count Directly From Tophat?
  I have been using HTSeq to count number of reads per feature for RNA-Seq. I am just wondering, Is...
• zeroes in ht-seq output
  I am using ht seq to analyse RNA- seq data for Drosophila. I have used GFF3 file as well as GTF f...
• Reference Genome file for assembly
   I am working on RNA-seq data analysis, but i am not able to get data of homo sapiens reference g...
• New to RNA-Seq: Reads assembled...now what? Non-sequenced organism. So lost!!
  Hello! Thanks for taking the time to read. I'm very new to RNA-Seq, and have been banging my head...
• Mir-RNA analysis by RNA-seq data
  Hello to all! I am gonna identify mir-RNA from RNA-seq reads, but it's the first time I am worki...
• GTF file for reference
  Hello, I have downloaded the reference for alignment of RNA-Seq with human transcriptome form[T...
• Homo_sapiens.GRCh38.91.chr.gtf.gz or Homo_sapiens.GRCh38.91.gtf.gz for differential expression of RNA-seq data?
  I am carrying out RNA-seq analysis and need the annotation in GTF format from Ensembl to go with ...
• Can I use own transcriptome without GTF file?
  I am a novice of RNA-Seq analysis. For differentially expressed genes anaysis, I am trying to run...
• How to create EGFP GTF file?
  Hi, I am analyzing RNA Seq data with EGFP. I need to get the count of EGFPs for samples. So I am...
• Advice : Building Transcript Models Using Cufflinks
  Hi Guys Keeping it short I want to know which is a better approach for building transcripts mod...
• What are the benefits of RNA-seq aligners that use GTF over just mapping to transcripts?
  In particular, I want to compare `STAR`, `BBMap`, and `BWA-MEM`. "`BBMap` is a splice-aware glo...
• Removing rRNA and tRNA sequences using GTF files
  Hello, The reference build on which I am currently working did not provide the FASTA files for ...
• Aligning RNA-seq and ATAC-seq gene annotations
  Hi, I have matched RNA-seq and ATAC-seq data from two cell subsets and I am trying to compare th...