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• 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 ...
• How to force BWA to generate SAM
  Hello, How to force BWA (version 0.2.3) in Galaxy to produce SAM files rather than BAM files? 
• 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...
• Sam To Bigbed
  Hi, Is it possible to generate a bigbed or bigwig file from SAM (or BAM) file using Galaxy? It lo...
• Bam To Sam
  SAM-to-BAM (version 1.1.2) says that it produces an indexed BAM file based on a sorted input SA...
• Using DEXSeq count on a sliced bam or sam file
  Using DEXSeq count on a sliced bam or sam file does not seem to run properly. The output file re...
• An error occurred setting the metadata for FIlter Bam/SAM files
  I am getting error in setting the metadata after filter BAM/SAM files. I tried using auto-detect ...
• Bed To Bam Conversion In Galaxy
  Is it possible to use some tool in Galaxy to convert BED file to Bam/ sam file. In other word do ...
• Unable to view aligned reads in IGB after loading BAM file
  Hello everyone, I downloaded an SRA file from a GEO accession and converted it to a BAM file usi...
• Displaying bam or bigwig files in UCSD genome browser
  Hello, I am attempting to view my RNAseq mapping file output (SAM) on the UCSC genome browser. T...
• 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...
• 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 ...
• Issues with SAM to BAM conversion
  I am receiving the following errors (below) when I attempt to convert my SAM file to a BAM file, ...
• sam to fastq
  Hi I have mapped PE reads to a custom build genome using bwa and converted the sam output to bam...