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• gene Id to gene name
  I did DEseq2 on galaxy for my samples after STAR alignment. I got the report and found the first...
• RNA-seq : problem with gene ID
  Hi all, It's the first time for me on galaxy and I have some problem. After the Deseq2 analyse...
• 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...
• gene names and gene ids
  hi i have a annotate file of vcf using vcf annotate and in my out i dont have any gene ids thier...
• salmon gene quant to DESeq2
  Hi again - I successfully ran salmon on my fastq files, including gene-level summary via a simpl...
• 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...
• snpEff gene names
  Hello! I am new to snpEff. I built my database for my sample using gff3 files created from PROKK...
• Cuffdiff output redundant genes
  Hello, I am using the Galaxy tool Cuffdiff to analyze the RNA-seq data. But for the output file "...
• htseq and cufflinks
  Hi, I have used HTSeq to count the no of mapped reads, the HTSeq gives me the ensemble ids but w...
• Mutliple UCSC gene names in RStudio Data Table
  Hi there, I am using the cummeRbund package in R Studio on my personal computer to analyze diffe...
• converty cuff id to gene id
  Hi, wondering if anyone could give me some clues how to convert cuff gene id to normal gene id so...
• Htseq-count: How to add id attribute and additional attributes in Galaxy (RNA-seq)
  Hello, I am working with a bacterial genome. I'm using DESeq2 for differential gene expression an...
• How Insert Gene Ids?
  Hi, I have used the RNAseq tools to calculate the FPKMs values, now I would like to know how I c...
• DESeq2 couldnt run due conflict in annotation
  Hi, I was trying to run DESeq2 but some error is happening: Error in summarizeToGene(txi, tx2ge...
• 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...
• Gene Names From Cuffdiff Data
  How does one get gene names when using cuffdiff when looking at "gene differential expression tes...
• Batch conversion of ID to gene symbol
  I'm an old school molecular biologist who studies gene expression but is quite new to bio-computi...
• Replicate Common Gene Names
  This is somewhat Galaxy related, but more of a general question. I did all of my mapping and ini...
• How to convert gencode ID into ENSEMBL ID
  Hi, I have gene Id derived from gencode and I am trying to convert into gene names, but i think I...
• gene names from ucsc id
  i have cufflink and cuffdiff output. i want gene names in ncbi ids and a tabulated format. i can ...
• Genomic Coordinates To Enterz Gene Ids
  I have a list of around 3000 genomic coordinates of mouse genome and I would iike to extract gene...
• 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 ...