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• Help
  Hi, I read on Readme for MACS that: "For the experiment with several replicates, it is recommende...
• Merging two fastq files together
  Hi all, I've recently received the .fastq files for my rna-seq experiment. According to the sequ...
• Macs Out Put Files From Galaxy
  I ran MACS on my chipseq dataset and found various files: 1. under html report there ar etwo fil...
• Cuffdiff
  Dear All I have simple and question for cuffdiff should we run cuffdif on merge transcript file (...
• Concatenate vs Concatenate (cat) Utility in Galaxy
  I see there are two wrapped tools under the Text Manipulation header for concatenating datasets, ...
• Concatenate fastq files in galaxy
  Hi, I have several fastq files that I want to merge. can anybody share how to concatenate multipl...
• Concatenating four Nextseq fastq files
  Hi, Please excuse my naivety but my sequencing was run on NextSeq with single end reads, I have...
• Which Concatenate tool help with an error in wig to BigWig conversion
  Hi there, I am not sure which concatenate tool to use to combine individual chromosome wig files...
• plotProfile/plotHeatmap - How to change the file names?
  I would like to compare H3K4me3 ChIP peaks of several samples at TSS. Therefore, I used "compute...
• Running multiple workflows with multiple inputs
  Hi, I recently learnt to create workflows and to script in galaxy using bioblend. Seems like a v...
• Chip Seq analysis with multiple biological replicates for differential expression
  Hello, I am very new to sequence data analysis and had some structural questions. I am trying to ...
• Text Editing
  Hello Luce, I can explain the use of the tools "Text Manipulation". For each file independently,...
• Need help with "Concatenate datasets" tool
  Hello, What is the difference between "Concatenate datasets tail-to-head" under "Text Manipulati...
• Assigning a "sample_name" column dynamically in the SAM tool generate pileup
  Hi everyone, I am creating a workflow in Galaxy that I will be using for variant analysis for ab...
• Chip-Seq Data
  Hi, I have illumina ChipSeq data in txt format with this structure: @HWI-EAS225:8:1:1:58#0/1 NAG...
• Data from NextGen sequencing uploaded, concatenated, but not in appropriate FASTA format for next step?
  Hello, I received my raw NextGen sequencing files and am following a lab mate's protocol based on...
• Cannot join combined R1 and R2 files
  Hi Everyone,   From reading around, I'm not sure whether a solution has been found to the probl...
• Extract gene sequence from BAM.
  Hi, I have several BAM files with different samples of a chromosome and I want to end up with one...