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• Help! I'm using trimmomatic in Galaxy, but it doesn't recognize a part of input dataset.
  I'm using Trimmomatic to trimming paired end reads. When I set "Single-end or paired-end reads?"...
• Dynamic Tool Parameter Lists based on an Input File
  What is the best way (or any way) to generate dynamic Galaxy tool fields based on data inside a s...
• Linked inputs in created workflow
  I have created a workflow with 9 steps. When I run my workflow the first 2 steps are to input dat...
• problems with Tophat2
  HI there, I am attempting to use Tophat2 (version 0.6) but when I select paired-end reads I don'...
• Tophat "Mean Inner Distance Between Mate Pairs"
  Hi all, When mapping pair end RNA-seq reads using tophat, we need to type in "Mean Inner Distanc...
• Problems with Bamtools: Filter BAM
  Hi, I seem to have a problem with filtering merged BAM files following a recent update. I am tr...
• Galaxy-using trimmomatics with ChIP seq pair ended (only one file with both reads)
  I am trying to run Trimmomatics in Galaxy under "pair end (as collection)" for afastqsanger.gz ...
• How to select multiples files as inputs to parse them simulaneously ?
  The question is in the title. I begin with Galaxy :) I want to make some statistics on several f...
• Pair end alignment using HISAT2
  Hi, I have a FASTQ file that is a paired library. I want to align this FASTq file to Hg19 genome...
• Quality Stat.
  Dear User, I am trying to use the tool "Compute quality statistics" in galaxy on Ilumina single ...
• Combining The Paired Reads From Illumina Run
  Hi, I have two fastq files with the forward(/1) and reverse(/2) paired reads. The reads are not ...
• Problem running CollectRnaSeqMetrics
  Hello, I am trying to run Collectrnaseqmetrics in usegalaxy (toolshed.g2.bx.psu.edu/repos/devtea...
• Input Merged and unmerged paired end read files into Salmon
  Hello, I have reads from three paired-end libraries and they have been merged, so for each libra...
• Galaxy: Check input file names are the same
  I would like to ask if it's possible to check the file name of an input dataset. I have this prob...
• Data collection and Tophat2
  Hi, I am trying to play with data collection (developped by John Chilton) and I am confused on h...