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• Duplicate Row Removal in Merged FeatureCounts
  Hello,   I am trying to transfer merged featurecount data into an R-studio package called RNASe...
• How to convert SAM file to tabular ??
  Hi everyone, I am trying to convert the SAM file to tabular ?? Does anybody know? Is there any ...
• Excel tab-delimited file not being detected as a tabular dataset
  Hi! I have an excel document containing DNA sequences which I am trying to convert into a tabula...
• featureCounts jobs will not submit unless input BAM(s) have the "database" metadata assigned
  Hello, I am trying to run featureCounts on my BAM file using a built-in genome from Galaxy. I wro...
• featureCounts 1.6.0.3 using reference annotation GTF from the history
  I used featureCounts about two weeks ago on one dataset and had no issues. Today I tried running ...
• using SAF gene annotation file in featurecounts
  Hello! I'm new to Galaxy and was wondering if I could get some help with using the featurecounts...
• Analysis of Galaxy Cuffdiff output by CummeRbund
  Hi, I am trying to use cummeRbund in Rstudio to analyse my Galaxy Cuffdiff output. However I am ...
• Locally cached annotation not available for featureCounts
  Hi all, For my RNAseq analysis, I am using the featureCounts tool to measure gene expression fr...
• Gene Ontology Help
  To Whom it May Concern: My name is Nicole McDaniels. I am a Ph.D. candidate at Syracuse Universi...
• Unable to select GTF file from history in featureCounts (Galaxy version 1.6.0.3)
  Hello, I have recently begun mapping Drosophila RNA-Seq data with STAR (in Galaxy), and I am now...
• Problems converting a file to FASTA
  Hello! How are you? I am having a hard time converting a file. I have  FASTA formatted sequences...
• Dynamic Options Not Filling In
  I am trying to use dynamic options in galaxy but it isn't working. Essentially a user can includ...
• FeatureCount output does not match view in IGV browser
  I have a BAM file that I view locally in IGV browser. Specifically, I am focused on hsa-mir-122. ...
• Scaffold making via scripting
  Hi  My question today is for experts using python programming to do Bioinformatic analyses. I am...
• Multi-join name of the dataset
  Hi, I am analyzing RNA-seq data on multiple fastq files. I processed all of them to get the Feat...
• Duplicate row names error with EdgeR on FeatureCounts files
  Hi all, I created tabular count files using FeatureCounts with a GTF file (iGenomes, UCSC hg38) ...
• Content of the built-in hg38 genome annotation available in Featurecounts
  Hello, After executing featureCounts on my BAM file using a built-in genome (hg38) from Galaxy ...
• Workflow only runs first step and then stops
  Hello, I am trying to learn how to process RNA-Seq datasets with Galaxy to compute read counts pe...
• files not found using Galaxy with Pulsar
  Hi, Hoping some can help me with my issue with Pulsar and Galaxy. I have installed tools and som...
• Are reads number normalized on transcript length ?
  Hello, I used featurecounts to obtain reads number from a RNA-seq file (.bam). I would know if t...
• Visualization Through Trackster On Local Galaxy Installation
  Hi, I am trying to set up the visualization functionality on our local Galaxy installation. I fo...
• Display data summary from R code in my galaxy tool
  I have created a galaxy tool, which get the gene expression data. I want to do some gene express...
• I am slightly confused about the input requirements for the differential expression tool - last step of Trinity
  Hello all, I have a pressing question... To start with, I have read the Trinity methods paper ...