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• 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...
• Combining Reads from 2 Lanes
  Hi, I'm running an RNA-seq analysis to look for differentially expressed genes. I'm using sing-e...
• combining FASTQ files from 3 lanes
  Hi, I have data from multiple samples that were multiplexed and split across 3 lanes. These we...
• 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...
• Mark Duplicates - MAPQ = 0 and Value was put into PairInfoMap more than once
  Dear Biostars Galaxy team, I'm relatively new to using the Galaxy online platform and have been ...
• Replicates
  Hi, I am trying to analyze some RNA-seq data using the Galaxy. The reads for each sample comes f...
• Select FASTQ reads by sequence
  Which tool should I use to select all reads from a FASTQ file which include any of about 100 shor...
• RNA seq beginner
  I just got back RNA seq data produced on the HiSeq 4000. They prepared the libraries and performe...
• Merge BAM files
  The Merge BAM files option is no longer available on NGS:Sam Tools. Where has it gone? How can I ...
• Problem concatenating different lanes
  Hi All,   I'm fairly new around here so I really appreciate all your help! I am trying to conca...
• How To Get Output From Galaxy
  Hi, I am a very new user at Galaxy. I have downloaded the Galaxy and am running it in my compute...
• Multiple fastq files in Bowtie2
  I have 4 lanes in each set of reads. I do understand using the multiple datasets option will run ...
• 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 ...
• 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...
• Re: Fastq To Fasta Tool
  Hi Omri, Thanks for reporting this issue. There were two different FASTQ to FASTA tools loaded ...
• 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...
• 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...
• Running multiple workflows with multiple inputs
  Hi, I recently learnt to create workflows and to script in galaxy using bioblend. Seems like a v...
• Selecting Reads At Random From Fastq File
  Hi, I am curious if anyone knows how to select random lines from a fastq file. There is a select...
• Merging two fastq files together
  Hi all, I've recently received the .fastq files for my rna-seq experiment. According to the sequ...
• 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...
• Merging BAM files: bamtools not found
  I have BAM files from aligning paired end Illumina reads. I would like to merge the aligned seque...