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• RNA seq beginner
  I just got back RNA seq data produced on the HiSeq 4000. They prepared the libraries and performe...
• Analysis of forward and reverse reads
  Hello. Newbie here: I have recently done some chip-seq, and for each sample, I have different ...
• 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 ...
• Combining Reads from 2 Lanes
  Hi, I'm running an RNA-seq analysis to look for differentially expressed genes. I'm using sing-e...
• 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...
• Need Help To Split Paired-End Dataset
  I am new to the NGS analysis. I need help to solve this problem. As shown in my previous emial...
• Forward and Reverse reads from paired end sequencing
  The fastq dataset we have after illumina whole genome sequencing is in the form of two files - fo...
• (No Subject)
  I am new to the NGS analysis. I need help to solve this problem. As shown in my previous emial...
• Illumina HiSeq reads and Fastq joiner
   Hello, I have paired-end reads (Illumina HiSeq) from a metagenome in two Fastq files. These non...
• Which Galaxy tool can concatenate fastq files from different lanes of flow-cell?
  Which tool on Galaxy can I use to merge my fastq files from lanes 1,2,3, and 4 of a single librar...
• Re: Getting Reference Index Files In Local Galaxy Install
  Hi, We have a local install of galaxy and I'm trying to add the reference index files for bwa usi...
• Can I Convert Paired-End Datasets Into Single End Ones?
  Dear All, I have some paired-end datasets to be analyzed, but I am not sure about their Mean Inn...
• Initial Qc And Grooming For Illumina Hiseq2000 Paired End Rnaseq Data
  I am trying to do RNAseq analysis on Paired end data from the Hiseq2000. I have about 50 files f...
• Fastq Splitter Empty And Fastq Manipulator Doesn'T Work
  I am having the same issue as this user: http://user.list.galaxyproject.org/FASTQ-splitter-produ...
• Merging BAM files: bamtools not found
  I have BAM files from aligning paired end Illumina reads. I would like to merge the aligned seque...
• Trimming And Thinning Of Paired-End Reads
  Hi galaxy users, I've been experiencing some problems trimming the adapters and filtering by qua...
• How do I combine multiple SE libraries in a single Trinity run?
  I have two SE librarys I need to assemble together with Trinity. Library one has 7928922 read pa...
• Remove "Unpaired" Reads From Quality-Filtered Pared-End Fastq Files.
  Hi there, I obtained two fastq files from GA paired end run. I filtered each file by quality usi...
• Multiple fastq files in Bowtie2
  I have 4 lanes in each set of reads. I do understand using the multiple datasets option will run ...
• 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...