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• illumina PE quality control - NGS: QC & Manipulation
  Hi, I have a PE illumina miseq data set (separate forward-R1 & reverse-R2) of a WGS of a par...
• Running Trimmomatic on loop for Paired End
  I'm need to do trimming for Paired End. Is there any way around where I can run the trimmomatic ...
• Cannot select fastq data in Galaxy Trimmomatic
  Hi Galaxy-verse I am trying to open my uploaded paired-end MiSeq reads in Trimmomatic from withi...
• Trimmomatic on paiera end data
  Hi I am trying to use Trimmomatic on my Sanger Illumina 1.9 paired end data. Trimmomatic ask fo...
• RNAseq data to be processed in two ways: (i) mapping to de novo Trinity-based transcriptome and (ii) mapping a relatively new genome
  Hello all, I am new to RNAseq data and learning this process step by step, so I have a few quest...
• Fastq Joiner
  I am trying to join two groomed fastq files from a paired-end Illumina read using the fastq joine...
• Paired-end imports produce 8 files. What to do?
  Hi all, I've been scouring the forum for the "first step" in importing fastaq.gz (which unzips au...
• 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-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 ...
• Bowtie2
  Hi All I'm trying to use bowtie2 in Galaxy but though I have uploaded a valid pair of fastq file...
• Illumina HiSeq reads and Fastq joiner
   Hello, I have paired-end reads (Illumina HiSeq) from a metagenome in two Fastq files. These non...
• Do I trim paired end sets first or merge and then trim?
  Hi there, I have a quick question - I have raw 10Gb -sized datasets for my samples. For each one...
• Fastq Joiner Problem
  Hi, I am trying to join two groomed fastq files from a paired-end Illumina read using the fastq j...
• Need help with "MACS" tool--program setting
  Hi, I have a question about running MACS tool for my chip-seq data to call the peaks for the tra...
• Can someone give me a foolproof instruction on how to merge R1 and R2 illumina fastq files
  Dear Galaxy experts,               I need to merge R1 and R2 Illumina paired end reads. T...
• Regarding splitter or merging the paired end sequencing file
  hello, Recently i got paired end data and firstly, i removed the adopter sequences. For that i u...
• Use paired collection on wrapper
  Hi, I'm try to write a wrapper for a tool that performed subsampling of fastq file. The script i...
• Paired end illumina RNAseq reads - running trinity with paired trimmed files and adding unpaired as single read?
  We have paired end Illumina HiSeq 4000 reads that we are working to remove adaptors and trim base...