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• Problem with Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region (Galaxy Version 1.1.1)
  First i don't know if this is the correct place to report tool problem. I did not get any bug dat...
• mtDNA demo SAM to BAM problem GALAXY
  Hello Folks, I've been trying to run through the GALAXY.org mtDNA workflow demo, the first one, ...
• 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...
• 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...
• SAM/BAM To Counts dataset generation errors
  When trying SAM/BAM to Counts I get the following error message:   pysam not installed; please in...
• 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...
• Flow issues? (no temp SAM/BAM to start run?)
  Hi, Trying to run a workflow. But cannot due to the insistence of cuffdiff on existence of SAM/B...
• Sam-to-bam in workflow
  I made a workflow in which I am using the tool SAM-to-BAM. I wanted to use a locally cached refer...
• 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 - Galaxy version 17.01
  Hi All First of all I am not a bioinformatician, I'm looking at someone else's test workflow. I ...
• 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...
• Problem With Sam-To-Bam Conversion
  Hello, I am trying to map Illumina paired-ends reads from the nematode Caenorhabditis briggsae. ...
• 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...
• Problem for converting SAM file to BAM file
  Hi,  Recently,galaxy always reports error when I convert filtered SAM file to BAM file by using ...
• fastq to bam
  Hi, I am a newbie in these bioinformatics tools. I have 42 x 2 (paired end) fastq files that got...
• sam to fastq
  Hi I have mapped PE reads to a custom build genome using bwa and converted the sam output to bam...
• Problem With Depth Of Coverage On Bam Files (Gatk Tools)
  Hi, I am trying to used Depth of Coverage to see the coverages is specific intervals. The interva...
• 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 ...
• 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...
• Sam To Bam Conversion Problem
  Hello Galaxy Support, I generated an alignment with a "fastq groomed" illumina dataset using the...