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• What format of data required for Mapping with Bowtie
      I am a new user of Galaxy. Recently, got some next gen RNAseq data from Illumina single end...
• reference genome not present in Galaxy
  good morning,   i would like to use Bowtie or BWA to map reads from Illumina sequencing to the ...
• Bwa Errors
  Hi, Two related issues: We tried to run BWA for Illumina on two groomed files (fastqsanger)...
• Duplicate Reads
  Dear all, When is it necessary to remove duplicate reads from your RNA Seq analysis? Is it requi...
• bowtie vs bowtie2
  Hi again! Thank you for being so prompt with the answers. I appreciate it. Question, if my read ...
• Problems Running Bowtie And Bwa
  I am trying to map fastq files using bowtie and bwa and the job will not run. It has remained gr...
• Built-in indexes not working in Local Galaxy Instance
  Hi, I've just finished setting up a local Galaxy instance and everything works fine except for b...
• Bowtie/Bwa Not Running
  I tried to start an alignment with bowtie and bwa last night, and they are still "waiting to run"...
• Mosaik With Paired Reads
  Hello, I'm trying to run Mosaik on our galaxy instance on Ilumina paired reads. However when I se...
• Re: Output File For Bowtie Suppressed Reads (-M/--Max)
  Hi all, I'm running into a problem with the output from bowtie mapping for illumina reads. I'v...
• Map With Bowtie
  Hi Colleagues, I mapped illumina sequences using Bowtie on Galaxy server, I could not locate the ...
• Gain Sequences After Mapping Reads To A Reference Genome
  Hi all, I would like to know if mapping reads to a reference genome, through galaxy, can generat...
• Aligning Long Reads
  Hi, I am new to mapping. I have reads ranging from 150-300bp, i am not sure which is the best...
• Galaxy Bowtie Alignment Stats Report
  Hello, Does anyone know how to get alignment stats from Bowtie on Galaxy? I would like to know w...
• how to extract mapped reads from output of BWA-MEM to a separate file?
  Hello all, By default, BWA-MEM on the main galaxy server does not seem to give an option to writ...
• Bowtie: Outputting Unmapped Reads
  I was hoping this question had been asked, but I haven't been able to find it. I want to output ...
• Bowtie
  Hi Experts, I have single end Illumina reads from ChIP-Seq experiment. The files have encoding I...
• Every job is waiting to run
  I wanted to upload mu trimmed reads to galaxy and map them using bowtie, but the only task I was ...
• BWA - History does not include a dataset of the required format
  Hello, I tried to aligned paired end reads with BWA (Map with BWA (version 0.2.3)) on my own Gala...
• Using Files Produced By "Barcode Splitter"
  I used the "Barcode Splitter" tool to split multiplexed RNA-Seq libraries into separate files. I ...
• MACS fails, finds peaks but can't build model
  Hi,  I'm using the Galaxy GVL-QLD instance.    I have single reads chip-seq files from E. coli...
• Extract fastq sequences from BAM with flag Supplementary alignment
  Dear all, after running BWA-MEM on a fastq dataset, I identified some "supplementary alignment" r...