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• Problem in genrating Correlation Plot
  I'm work on differential gene expression. I do have Tophat and cuff link files. I'm not able to g...
• Error when trying to create heatmap
  Hello. I am new to galaxy and trying to learn. I am trying to recreate the heatmap here: http:...
• deepTools computeMatrix sorted values WITH gene identifiers
  I've performed a computeMatrix analysis on a ChIP-seq sample referenced to gene TSSs. This genera...
• Heatmap of numeric data tool produced error (usegalaxy and local)
  Hi, I got the following error on usegalaxy and also on my local galaxy: bash: /galaxy/main/s...
• Error - Heatmap generation / visualization from RNA-seq data using DESeq2 workflow
  Hi I wanted to try generating heatmaps of gene expression using normalized counts file obtained ...
• Heatmap using cummeRbund
  Hello, I want to do a heatmap using cummeRbund. Is it possible to select a set of genes (for e...
• quantifying differential gene expression across three groups using cuffdiff
  Hello, I am trying to identify differentially expressed genes across three groups.  The groups c...
• Papillon: a python alternative to plot/heatmap Galaxy RNA-seq data
  Hello, I learned how to do a RNA-seq using Galaxy, without use the terminal. But then, we you wa...
• Using different reference genome yields different results in RNA-seq data analysis
  Hello, I've got some questions with my RNA-seq results generated by galaxy.  For the experiment,...
• How to determine genome wide Co-occupancy between two transcription factors? by Galaxy main
  Hello: I am currently using Galaxy to analyze several sets of ChIP-Seq datas, including those pu...
• htseq and cufflinks
  Hi, I have used HTSeq to count the no of mapped reads, the HTSeq gives me the ensemble ids but w...
• Creating Heatmap from RNA-seq
  How to create a heatmap using RNA-Seq data? We analyze the RNA-seq using Tophat-Cufflink-Cuffdiff...
• featureCounts gives extreme low counts on highly expressed genes
  I mapped paired-end sequencing with RNA-STAR and got the BAM file. I then use featureCounts to co...
• How can I merge two single-end mapping data
  Hi, I am analysing my ChIP-Seq data which generated by paired-end sequencing. But due to some ex...
• computeMatrix skipping bug is causing a problem with large data sets
  When running computeMatrix with a large set of data I keep receiving this error multiple times ea...
• 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...
• how prepare File containing a mapping of transcripts to genes under Salmon
  Hi, I don't know exactly which columns should be put for Salmon to convert transcript to the gen...
• 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...
• Issue running Cuffdiff using Cuffmerge gtf output
  I am trying to use Cuffdiff to find significant changes in mRNA transcript expression between two...
• Htseq-count input data
  Dear colleagues, I am a new Galaxy user motivated to exploit its tools to compare two sets of the...
• Alignment and consensus from mapped reads (Ion PGM - Ampliseq Custom Panel)
  I have an Ion Torrent Ampliseq Custom panel of 28 Culex genes that I have run on our Ion PGM. It'...