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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?"...
• Trimmomatic output after filtering paired end data - fastqsanger vs fastqsanger.gz
  After running Trimmomatic on a paired end PolyA RNA-seq dataset where both forward and reverse re...
• 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 ...
• 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...
• 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...
• Splitting Biased Paired End FASTQ data
  The FASTQ splitter in Galaxy warns that the tool only works if Paired-end data has equal length r...
• Trimmomatic and Trim Galore are not working.
  I am performing an RNA-seq and am trying to trim adapter sequences with Trim Galore. When I made ...
• fastq splitter problem
  fastq splitter is not working on paired end read for some of my file and produce output file with...
• Nextera pair end adapter cleaning
  Can I use Nextera pair end adapter option in Galaxy Trimmomatic program for cleaning my illumina ...
• Help with downloading files from EBI SRA
  I am new to galaxy and have been trying to figure out how to align RNA-seq reads to a genome in o...
• Trimmomatic on paiera end data
  Hi I am trying to use Trimmomatic on my Sanger Illumina 1.9 paired end data. Trimmomatic ask fo...
• my tool and collections
  Hello, I want to do something related to writing my own tool (in perl) and 'collections'. I have...
• Data collection and Tophat2
  Hi, I am trying to play with data collection (developped by John Chilton) and I am confused on h...
• Kraken (assign taxonomic label...)
  One Illumina file fastq.gz contain all info about paired-end reads. I used by usegalaxy interface...
• Trinity run preprocessing
  I am new to Trinity and galaxy instance (https://usegalaxy.org/). I have 17 samples pair ended. I...
• filtering pair-end bam file
  Hello, I am trying to filter a pairend bam file to get only forward reads in Galaxy. A bam filter...
• 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 ...