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• Need help with "MPileup" tool
  I am trying to get SNPs and indels from a bowtie 2 on Illumina reads matched to the sinorhizobium...
• Trouble with samtools mpileup when I supply my own reference genome
  I've been working on Galaxy to run samtools mpileup function. When I use the supplied reference g...
• MPileup calling every base as <X>
  Having a few teething problems on my first use of Galaxy (surprise!)   Workflow as follows; Up...
• Suggestions for variant callers/ problem with BCF view
  Samtools mpileup only outputs genotypes fields for samples when a BCF output is selected. The BCF...
• How to add flanking sequences to SNPs from vcf files
  Hej, I posted this question in Biostars nad would like to shift this post here to biostars galax...
• Need help with mpileup tool on Galaxy
  Hey, I'm new to bioinformatics and I'm having some trouble creating an mpileup. Trying to create ...
• Mpileup with vcf output?
  Hello, I noticed that the "mpileup" tool that gives an output file in vcf format is no longer av...
• SnpEff (Galaxy) troubleshoot
  I have got Mpileup data. I wish to further understand SNP effect using snpeff. Unfortunately, in ...
• Listing genome reference
  Hi, I would like to map reads against genome reference but my genome of interest is not listed. I...
• vcf to fasta
  Hi,   i want to generate fasta files of my mapped sequence rather than the reference genome: s...
• Want all counts on MPileup including zero counts
  I am using the SAM tool MPileup application. The analysis parameters I use gives as an output th...
• BCFtools output tabular
  Hi, I'm sorry for my naive question (but this is my first analysis)... Analysis: 19 PCR targett...
• Error In .Vcf .Bcf Files From Freebayes And Mpileup
  Hi, I run a very regular BWA mapping with a public reference genome sequence and then I tried to ...
• Other reference genomes not listed
  Hello, I really like Galaxy tool but I have the problem that it does not contain the reference g...
• Galaxy GATK no reference genome availiable
  I would like to try the NGS: GATK Tools (beta) in usegalaxy.org, but there is no available refere...
• What is causing this MPileup error in Galaxy?
  Hello, I'm new to galaxy and next gen sequencing.  I'm trying to generate a VCF file from whole ...
• Multiple fastq file for mapping with Bowtie2
  Hi,   I have some amplicon sequences for 144 samples that I would like to map on to a reference...
• Sample Order in MPileup
  Hi Galaxy users! I'm attempting to call variants from targeted amplicon sequencing, and ran MPil...
• GATK tools and reference genomes
  The GATK tools are present as a beta version, and I tried to use selection or filtration, and the...
• How To Extract Geneid From Pileup File?
  Dear galaxy-users, I am working on a project to identify and genotype SNPs in targeted genes. ...
• mpileup error: reference sequence is not being fetched correctly?
  Hi, I ran mpileup using Arabidopsis reference sequence but got an error message in the log file w...
• Mycoplasma Pneumoniae M129 And Fh Reference Genome
  Hello! I noticed that Mycoplasma pneumonia M129 and FH are not found in the refe...