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• Combining Reads from 2 Lanes
  Hi, I'm running an RNA-seq analysis to look for differentially expressed genes. I'm using sing-e...
• Analysis of forward and reverse reads
  Hello. Newbie here: I have recently done some chip-seq, and for each sample, I have different ...
• Merging two fastq files together
  Hi all, I've recently received the .fastq files for my rna-seq experiment. According to the sequ...
• 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...
• 'Sampling' Bam or BigWig files?
  I am involved in an RNAseq project in which mutliple tissues of an organism are being analysed. N...
• Cannot join combined R1 and R2 files
  Hi Everyone,   From reading around, I'm not sure whether a solution has been found to the probl...
• Replicates
  Hi, I am trying to analyze some RNA-seq data using the Galaxy. The reads for each sample comes f...
• combining indexed paired reads from two lanes of a Hiseq rapidrun
  Hi I am doing paired end RNAseq, I have a single multiplexed pool that was run over both lanes o...
• RNA seq beginner
  I just got back RNA seq data produced on the HiSeq 4000. They prepared the libraries and performe...
• variable, low alignment rates with HISAT2
  Hello, I have some single end mouse RNA sequencing data that I would like to use galaxy to analy...
• Joining multiple fastq files that are spread across two lanes
  Here is a screenshot of my data https://gyazo.com/90183f5cc58ef9aed362658e24ebf9c1 I know how to...
• Multiple FASTQ files per replicate
  Hi There, I'm running an RNA-seq analysis using FASTQ data from an Illumina HiSeq Rapid V2 machi...
• Merge RNA-Seq files in CLC Genomics Workbench ?
  Hi I now analyzing my RNA-Seq data (illumina, 50bp paired end) using CLC Genomics Workbench to ve...
• Running multiple workflows with multiple inputs
  Hi, I recently learnt to create workflows and to script in galaxy using bioblend. Seems like a v...
• Multiple fastq files in Bowtie2
  I have 4 lanes in each set of reads. I do understand using the multiple datasets option will run ...
• Extract reads in FASTQ/A format from NCBI SRA
  Hi. I downloaded an SRA accession. In the results, the spots were separated but is in the same fi...
• how to perform alignment using Hisat2
  Actually I have several questions to ask but I try to be very much to the point. I want to uploa...
• Question About Sorting Barcoded Sequences
  Hi, I have an Illumina HiSeq lane of sequences, in which I input multiple samples with 5-prime 6 ...
• Can anyone share a workflow of differential gene expression on multiple conditions (>3) and triplicates?
  Hey guys, I just started using Tophat-cufflink on Galaxy today. But the example I found was quit...
• Data from NextGen sequencing uploaded, concatenated, but not in appropriate FASTA format for next step?
  Hello, I received my raw NextGen sequencing files and am following a lab mate's protocol based on...
• Merging BAM files: bamtools not found
  I have BAM files from aligning paired end Illumina reads. I would like to merge the aligned seque...