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• SAM-to-BAM error with custom reference
  Dear Galaxy Biostar team, I'm seem to be having a problem running Samtools SAM-to-BAM conversion...
• Ngs: Indel Analysis Tool Order
  Hello! I have a question about the NGS: Indel Analysis toolset in Galaxy. I hav...
• Problems With Picard And Gatk Tools
  Dear all, I have been trying to analyze some recently acquired WGS reads (re-sequencing with MiS...
• Sam To Bam Conversion Problem
  Hello Galaxy Support, I generated an alignment with a "fastq groomed" illumina dataset using the...
• Map with BWA-MEM local cache load option not available
  Reference: https://vimeo.com/123108417 Time location in video: 00:39 This video d...
• Problem With Sam-To-Bam Conversion
  Hello, I am trying to map Illumina paired-ends reads from the nematode Caenorhabditis briggsae. ...
• BAM to VCF format
  I'm analyzing NGS data on website:usegalaxy.org in the following steps: 1. Fastq file Raw reads Q...
• GWAS: Fastq to BAM to VCF
  I'm analyzing NGS data on website:usegalaxy.org in the following steps: 1. Fastq file Raw reads Q...
• Help W Sam To Bam
  Hi, We're loving Galaxy. This is an excellent interface and set of tools. The issue we're havi...
• Getting all unmapped reads
  I have a fastqsanger dataset from an RNAseq experiment, and I am trying to remove contaminating h...
• Mapping Illumina Reads Using Lastz
  Hello, I am trying to map metagenomic Illumina reads to the reference genomes. I used Galaxy LAS...
• 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 ...
• Problem Uploading Bam And Bai Files
  Hi, I've searched the archives and cannot find my situation. I have an Illumina MiSeq dataset wi...
• Question: SAM-to-BAM: fatal exit code Error 139
  Dear All, I am analyzing DNAseq data. I obtained a SAM file by using "Map with BWA for Illumina ...
• sam to fastq
  Hi I have mapped PE reads to a custom build genome using bwa and converted the sam output to bam...
• Using BWA with Illumina data and metagenomic "reference genome"
  Hi, I'd like to try using BWA to align Illumina reads to some contigs a collaborator made from my...
• 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...
• Using Segments Of Sequences As A Reference Genome - Bowtie For Illumina
  Dear all, My problem seems like something that should have a very simple solution from my end and...
• Count intervals of non-uniquely mapped reads overlapping the genome
  Hello everyone, I have some SAM/BAM files containing the alignments of small RNA-seq reads to mm...
• What is the difference between the tools "BWA" and and "Map with BWA for illumina" - tolerated mismatches at sequence end
  Hi, What is the difference between the tools "BWA" and and "Map with BWA for illumina"  ? I rea...
• 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 'Failed runtime validation of Using reference genome' Error - Local Galaxy instance
  Hi, I'm trying to run a workflow on a local Galaxy instance that has these steps in the beginnin...