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• Ngs: Indel Analysis Tool Order
  Hello! I have a question about the NGS: Indel Analysis toolset in Galaxy. I hav...
• 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 ...
• How to calculate the Average Insert Size after mapping the reads to the reference genome using BWA
  Hi everyone, Having mapped the reads (paired-end) to a reference genome using BWA, I am trying t...
• Extracting Reads Mapped From Bwa Mapping
  Hello, I recently figured out how to filter the output bwa SAM file for flag type in order to de...
• Are all the starting BED coordinates generated by BWA matching the first base of the reads ?
  I am currently using "Map with BWA for illumina" (in galaxy main server) with default settings to...
• How to convert SAM file to tabular ??
  Hi everyone, I am trying to convert the SAM file to tabular ?? Does anybody know? Is there any ...
• BAM to VCF format
  I'm analyzing NGS data on website:usegalaxy.org in the following steps: 1. Fastq file Raw reads Q...
• Problem With Sam-To-Bam Conversion
  Hello, I am trying to map Illumina paired-ends reads from the nematode Caenorhabditis briggsae. ...
• 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...
• 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...
• Mapping using multiple reference sequences
  Hi I am using BWA to map my FASTQ files against two different reference sequences (V3-1 and V3-2...
• How to create and run a pipeline using BioBlend and Galaxy API?
  I need to build the following pipeline: 1. Upload an SRA file from a remote FTP server (with an...
• export consensus sequence
  Hi, I have been using Galaxy.org for a couple of months now. It is such a powerful platform. I ...
• sam to fastq
  Hi I have mapped PE reads to a custom build genome using bwa and converted the sam output to bam...
• 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 ...
• 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...
• how to relate BWA input parameters to get minimum coverage and identity
  Hi all and thanks in advance for any help you will kindly provide. I'm aligning some short seque...
• Force galaxy to use the python 2 version of a dependency of a new tool
  I am creating a new tool for galaxy based on the NEAT-genReads tool from Zachary Stephens and I a...
• BCFtools output tabular
  Hi, I'm sorry for my naive question (but this is my first analysis)... Analysis: 19 PCR targett...