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• sam to fastq
  Hi I have mapped PE reads to a custom build genome using bwa and converted the sam output to bam...
• SAM-to-BAM; an error occurred setting the metadata for this dataset.
  Hi. I am very new to Galaxy and am following a simple workflow for processing FASTQ files: Step ...
• Sam To Bam Conversion Problem
  Hello Galaxy Support, I generated an alignment with a "fastq groomed" illumina dataset using the...
• Convert SAM to sorted BAM
  I am looking for a tool to convert SAM to sorted BAM (sorted by the coordinates, such as with sam...
• Low data conversion rate for BAM-to-SAM. Fix Database, Datatype, Sorting
  I have WXS fastq files from an illumina HiSeq 4000 paired end run- I uploaded them through FTP as...
• BCFtools output tabular
  Hi, I'm sorry for my naive question (but this is my first analysis)... Analysis: 19 PCR targett...
• fastq to bam
  Hi, I am a newbie in these bioinformatics tools. I have 42 x 2 (paired end) fastq files that got...
• using SamToFastq 1.136.0 in Galaxy workflows
  Hello, How can I connect in the workflow SamToFastq and Bowtie2 tools in Galaxy? I am trying to ...
• bam_index_build2() not yet implemented exception on local Galaxy instance - sam-to-bam
  Hi, I'm trying to run a basic workflow consisting of just Map with Bowtie for Illumina, Filter S...
• VCF output from Mpileup tool
  Hi everyboy, I am trying to call SNP using the SAM Tools → mpileup in Galaxy. Since the input ...
• Bam To Fastq Conversion
  I have a bunch of BAM files that I need to convert to FASTQ, are there such tools in Galaxy?
• SAM/BAM To Counts dataset generation errors
  When trying SAM/BAM to Counts I get the following error message:   pysam not installed; please in...
• BAM to VCF format
  I'm analyzing NGS data on website:usegalaxy.org in the following steps: 1. Fastq file Raw reads Q...
• Multiple alignment for fastq files from illumina
  Can I make a multiple alignment in Galaxy with fastq data from illumina? Clustal tool only takes...
• Conversion of SAM to BAM file
  SAM file is converted into BAM file but problem is that it cannot be open in galaxy. How it will ...
• galaxy biomina RSeQC bam/sam mapping stats error
  I am trying to run the Galaxy Biomina RseQC BAM/SAM mapping quality stats I have selected my upl...
• SAM-to-BAM (NGS: SAMtools)
  I am trying to convert my SAM file to BAM file and I want to use the built in genome, but there i...
• User Reference Vs. Built-In Index
  Hi. I created a workflow to map IGA reads using bowtie and generate a pileup at the end. The work...
• SAM to BAM conversion
  I have seen that I am not the first one to have the problem: the SAM to BAM conversion (either di...