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• 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...
• BWA-MEM Tool not recognizing fastq inputs
  I am attempting to use the NGS mapping tool BWA-mem. I have uploaded my reference genome, in addi...
• BWA-MEM Fatal error: Matched on ERROR
  Hi, I was aligning with bwa-mem on a 52.7GB trimmed paired fastq from WGS under the following con...
• Problem running BWA-MEM mapping
  I am trying to run BWA-MEM mapping in galaxy. I have uploaded FASTQ files using fastqcssanger and...
• Error running BWA-MEM or Bowtie2 in usegalaxy
  Hi, I am getting following errors while trying to run BWA-MEM or bowtie2 in usegalaxy. The input...
• 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...
• cannot align my fastq files
  i have two data sets of fastq type but i cannot align them with any aligner on galaxy tools as no...
• 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 ...
• 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...
• bwa not recognizing fastq files
  I am trying to map a set of fastq sequences to a custom genome, using BWA. The two setrs of trip...
• 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'...
• 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...
• Mapping paired reads to reference genome, variant calling
  I am trying to map a trio of paired-end Illumina reads to a reference genome, then identify polym...
• 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...
• mixing collections and "multiple" input tools
  I'm trying to modify a workflow to work on list collections. Most tools work as expected without ...
• Custom galaxy tool: multiple output files
  This is my first attempt to install a custom tool on galaxy and I'm having some trouble getting *...
• Galaxy workflow inputs
  I guess this is a stupid question because I couldn't find anybody else asking the question and it...
• Insert sizes in Galaxy
  I am new to RNASeq analysis. I used tophat to generate BAM files from FASTQ files but in the para...
• 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...
• no fastq data set available
  Hi, New to this program. Have my files uploaded in the history and have also made a dataset. How...
• Bowtie2/FreeBayes/mpileup variant detection on NGS of PCR amplicons around Cas9/CRISPR indels
  Hey threre, I have an MiSeq experiment using 24 indices where in each index I was sequencing 3 P...