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• DESeq2 couldnt run due conflict in annotation
  Hi, I was trying to run DESeq2 but some error is happening: Error in summarizeToGene(txi, tx2ge...
• Deseq2 give me sequence instead of gene ID
  Hi everyone, I am using deseq2 to test differential expression from salmon files (TPM) with a r...
• Annotation file formats .gff3 to .gtf conversion
  Dear all, I used the Galaxy tool to convert the .gff3 annotation file to .gtf format. Going thro...
• Stringtie Deseq2/EdgeR count tables all zero
  Dear Galaxy Team, I encountered a different problem with Stringtie + output additional files for...
• Converting transcript data from Salmon to gene level TPM
  I have got TPM data from running Salmon on RNA-seq data. However, this is TPM for each individual...
• How do I obtain gene names from ENSG values?
  Hi I have performed DGE using DESEQ2 (input htseq-count, following mapping by BWA-MEM) and have ...
• salmon gene quant to DESeq2
  Hi again - I successfully ran salmon on my fastq files, including gene-level summary via a simpl...
• Rna-Seq Analysis
  Since the pictures are too big for the mailling list. I will upload it in seperate emails. Dear ...
• Rna-Seq Analysis
  Dear all, I am using Galaxy for RNA-Seq analysis. I expect two lists: differentially expressed tr...
• Different RNA-seq result when I look at the gene_differential file and the transcript_differential file generated by cuff-diff
  Hi, I am wondering what is the exact difference between the gene list of the **transcript differ...
• what is a "Tabular file with Transcript - Gene mapping" in DESeq2?
  I have RNA Seq data from two conditions using a non-model organism. I constructed a trinity assem...
• (No Subject)
  Hi, I am playing with Galaxy ahead of getting ChipSeq data and it looks brilliant (thanks)... I...
• Give a list of genes and return Transcription starting sites as a bed file
  Dear there: I have a questions that may seems naive to most of you: does anyone know if there is...
• Fatal error with DESeq2 when processing TPM-based Salmon files and using a tabular transcript-gene mapping file
  Hi there, I have used Salmon to map RNAseq reads to a transcriptome. I then proceeded to anal...
• Ensembl numbers to gene symbols
  Hello, I performed RNA Seq analysis using DeSeq2. At the end of the analysis it got differential...
• Getting Figures from R with Galaxy DESEQ2 output?
  Hi, So this summer I ran a bioinformatics workflow on differential gene expression in three samp...
• Questions On Cuffdiff Output And Browser Visualization
  I would really appreciate someone's input on some issues I am having with my cuffdiff output for ...
• Difference between mRNA, CDS, transcript and gene in annotation file
  Hi, I am new to bioinformatics and have a very basic question. In the annotation files (gff) ava...