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• export consensus sequence
  Hi, I have been using Galaxy.org for a couple of months now. It is such a powerful platform. I ...
• BAM header using BWA-MEM in galaxy compared with GATK resource bundle (hg38) - deprecated tools in Galaxy
  Hi! I am trying to perform some analysis using GATK in order to identify mutations. Long sotry s...
• FASTAQ not able to be selected in BWA, though FastaQC passed
  I need some help. I am trying to map two fastq datasets with Bwa-mem. If I design a workflow by...
• Problem running BWA-MEM mapping
  I am trying to run BWA-MEM mapping in galaxy. I have uploaded FASTQ files using fastqcssanger and...
• Can we map fastq files with paired ends using bwa mem on galaxy?
  I have a collection of timmed fastq files from WES, each contain paired ends. Is it possible to m...
• bwa-mem installation and use
  Goodmorning, (sorry for my bad english), I would use bwa-mem in Galaxy to map sequences against h...
• bwa mem index builder error
  I would like to use the BWA mapper tool so I installed the tool "bwa" from "devteam" from main to...
• Queue time for tool "NGS Mapping: Map with BWA-MEM" at http://usegalaxy.org
  The past 2 nights I've attempted to follow the steps outlined in: http://nekrut.github.io/BMMB554...
• BWA-MEM mapping Taking longer time
  Hi Folks, I am trying to run BWA-MEM mapping, its taking longer time. Can you please look into i...
• Not able to run BWA
  I'm trying to run BWA-MEM using Galaxy. I have a reference.fastq (I built a custom reference) and...
• Using the Extract Genomic DNA tool in Galaxy
  Hi everyone! So I am trying to use the the NGS: SAMtools function in galaxy to generate consensu...
• Using BWA-MEM to align fastq files from MinION
  I am trying to use BWA-MEM in Galaxy to align fastq files to mouse genome. I am having an issue w...
• Alignment and consensus from mapped reads (Ion PGM - Ampliseq Custom Panel)
  I have an Ion Torrent Ampliseq Custom panel of 28 Culex genes that I have run on our Ion PGM. It'...
• bwa-MEM fails to execute with reference sequence (hg19.fasta) from history
  Hi, I have been trying to use custom reference genome hg19.fasta and choosing the option to buil...
• 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...
• Can't run files successfully using BWA-MEM
  Hi I am currently working on a course project. Using the main galaxy server, I am having issues ...
• Create and extract consensus sequence after initial genome mapping using a custom genome
  I have aligned fastq sequences (from an insect vector) to a small bacterial genome of 1.2 mb (as...
• Checking coverage of yeast whole genome sequencing data
  I have WGS data (2x150b paired end NextSeq reads) for Yeast (sacCer3) and would like to know how ...
• How to Realign Indels and logic of workflow
  I have paired end reads of a trio that I eventually need to call variants on (make a .vcf). So I'...