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• 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...
• 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...
• 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...
• Error message: This job was terminated because it used more memory than it was allocated
  Hi,  I'm processing exome data (enriched with Nextera kit) in Galaxy. After mapping the reads us...
• 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 ...
• Problem running BWA-MEM mapping
  I am trying to run BWA-MEM mapping in galaxy. I have uploaded FASTQ files using fastqcssanger and...
• sam to bam - Galaxy version 17.01
  Hi All First of all I am not a bioinformatician, I'm looking at someone else's test workflow. I ...
• 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...
• Samtools error assoicated with multiple mapping tools
  Hoping for some help here. I am having issues with several mapping tools that utilize samtools a...
• 'print reads' throwing 'eof marker is absent' on my BAM file
  Yes I've read many of the posts out there about 'BAM EOF absent', but can't find a resolution. I...
• samtool sort error in sorting BAM files by read name
  Hi, I'm trying to sort my BAM file by read names (-n) on Galaxy but it gives me this error: [bam...
• 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'...
• Problem with can't allocate memory
  Hi all,  After Map with BWA-MEM run successfully, it provides the following message "Generating ...
• BAM files fail to be recognized
  I generated BAM files on galaxy using BWA-MEM. I am trying to run BAMtools, Picard, etc on them. ...
• BAM files on IGV look empty
  Thanks for your previous help. I use these demonstration files https://zenodo.org/record/582600#....
• 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 mapping Taking longer time
  Hi Folks, I am trying to run BWA-MEM mapping, its taking longer time. Can you please look into i...
• Having trouble viewing mpileup
  I have generated an mpileup using one bam file, just wondering what is the best way to view this?...
• FASTA consensus from BWA-MEM mapped MinION data?
  Does anyone know how I can I generate a FASTA consensus from BWA-MEM MinION data using Galaxy?
• HISAT2 Output in Galaxy vs Command Line
  In galaxy, I am given a BAM and BAI file. Does galaxy implement the sorting and index function th...
• map with bwa-mem error
  Could not determine BWA version Traceback (most recent call last): File "/Users/shed_tools/toolsh...