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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...
• Cufflinks C. elegans no gene names?
  Hello, I have a question regarding cufflinks. I used HISTAT2 for alignment using this file - c_el...
• 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...
• How to get gene sequences (DEGs) not transcripts sequences?
  Hello, my name is one of Galaxy user in Korea. I conducted cuffmerge -> cuffquant -> cuff...
• 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 annotation for cuffdiff/cufflink
  I was wondering how to get gene "name" annotated to the cuffdiff. I used mm10 as the template, an...
• DESeq2 Gene IDs
  I recently ran DESeq2 and got GeneID's that look like this... AY172335.1 GL456164.2 ...
• 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...
• Gene name annotation
  Hi, I've done cufflink-> cuff merge-> cuffdiff finally, I used reference annotation huma...
• Getting Error In Bismark
  I am getting this error at the top while opening Bismark Mapper: Data table named 'bismark_bs_ind...
• Simplejson Reimport Error
  /home/www/galaxy/lib/galaxy/eggs/__init__.py:529: UserWarning: Module simplejson was already impo...
• Gene And Transcript Names From Cuffdiff
  Hi all, I am learning how to use Galaxy to analyze my RNA-Seq data. After running cuffdiff, one ...
• htseq and cufflinks
  Hi, I have used HTSeq to count the no of mapped reads, the HTSeq gives me the ensemble ids but w...
• Naming Maf Blocks
  Dear all, I heve done this in steps: 1. Go to genome.ucsc.edu and select the tables link. 2. Sel...
• How to covnvert gene id to gene names
  Hi, I have been using Tophat, cufflink, cuffmerge and cuffdiff to analyse RNA seq data. I hav...
• VCF gene name sorting
  Hello, I have a vcf file and need to tie it to the gene name. I did this with the vcf annotate t...
• How to extract information from a VCF file
  Hi everyone, I am currently taking an online tutorial on Galaxy and I have managed to complete s...
• Ensembl numbers to gene symbols
  Hello, I performed RNA Seq analysis using DeSeq2. At the end of the analysis it got differential...
• 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...
• Hidata
  After running Cuffdiff, I got more than 95% of genes with HIDATA status. What should I do?
• Is this correct way ??
  Dear Sir, while doing RNA-Seq analysis, after mapping, i have downloaded mouse reference gene se...