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• 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 ...
• 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...
• Nextera pair end adapter cleaning
  Can I use Nextera pair end adapter option in Galaxy Trimmomatic program for cleaning my illumina ...
• Illumina Clip Step in Trimmomatic
  In trimmomatic, under Perform Initial Illumina Clip step, which adapter sequence should I specify...
• how do I add cutadpat in online galaxy (not local) installation ?
  Hi, how do I add "cutadpat" in online galaxy (not local) installation? I have single end mirna se...
• trimming adapter sequences. is it necessary?
  Hi, I am a beginner to chip-seq analysis using Galaxy. I have received my data and did fastqc qua...
• Trimmomatic and adapters
  Hi all, As relatively new within the bioinformatics world, I am a bit confused when it comes to ...
• How do i remove multiple adapter sequences from my RNAseq reads?
  Hi there, I want to remove the universal adapters as well as the index adapters in each data fil...
• >90% aligned concordantly 0 times ChIP-seq Bowtie2
  Hi, I know this question have raised many times here and in other forums but I've tried everythi...
• Trimming And Thinning Of Paired-End Reads
  Hi galaxy users, I've been experiencing some problems trimming the adapters and filtering by qua...
• Read length from HT-Seq
  Hi, Sorry for asking this very basic question. I have paired-end RNA-Seq data. After initial ada...
• Pre-Processing Of Illumina Rna-Seq Paired End Data
  Hello, I have Illumina 76bp paired end data for a zebrafish RNA-seq experiment and am basically ...
• 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...
• FASTQC for RNA-Seq data in Galaxy
  Hello, I have 3 paired end fastaq file and when i loaded to Galaxy through EBI-SRA, it shows XX...
• 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...
• Trim Adapters And Other
  Hi, all! I have a maybe naive question that might be not so related to Galaxy usage. So I got th...
• 3' Adapter Trimming Using Fastx-Toolkit Clipper
  Hi all, I am analyzing miRNA sequencing now. My data is 51bp, single -ended and ~5 M reads. I wan...
• 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?"...
• trimgalore on interleaved paired-end fastq files
  Hi, I'm analyzing interleaved paired-end fastq files downloaded via fastq-dump. I am trying to r...
• How can I improve my mapping alignment rate with MiSeq 2x300 bp paired-end reads?
  Edit 1: it appears I have misinterpreted the raw data, which in turn led to my poor results. The ...
• 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 ...
• Trim Galore version - Adapter sequence
  Hello, I have been using Galaxy's Trim galore for clipping adapters from Illumina small RNA sequ...
• Trimmomatic Input Values
  Hello- I am using Trimmomatic to improve the quality of my RNA-seq data. I am using the followi...