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• Filter Pileup Error in SAMtools
  Hi, I am a new user to Galaxy and am having trouble with a filter pileup error. The error messag...
• Sam Tools Pileup
  Can we use the SAM tools pileup tool in Galaxy to get an accurate count of the coverage across th...
• Question: Problems with Filter pileup when performing Heteroplasmy tutorial
  Hello Galaxy, I am trying to do the Heteroplasmy tutorial from the tutorial page so that I can u...
• Deletions
  I have a DNA seq data set from mouse genome that is heterozygous for a known 15 bp deletion. The...
• Ngs Sam Tools: Filter Pileup Tool Not Working
  Hello, I am currently using galaxy main to run a filter pileup on datasets that used the generate...
• pileup to vcf
  Is there a tool on public galaxy that will take pileup file or filter pileup output to VCF?
• Filter Pileup In Sam Tools
  NGS: SAM Tools I have generated a simple 6 column pileup from my BAM file but when I try to use ...
• Converting Pileup Files To Wig/Bigwig
  Hi, I was wondering if you have a tool that converts pileup files to variable step wigs so I can ...
• Cannot filer pileup result
  I did MPileup, and I want to filer the pileup result to find the information I needed. However, t...
• Why Is 'Filter Pileup' Not Recegnising My 'Generate Pileup' File?
  Hi, I was wondering if you could help me with a problem I have been having recently. I have ca...
• Filtering Pile-Up Fails
  Dear All, I have been successful by using the online tool to align Illumina pair end reads , eac...
• Pileup Analysis
  Hello I was wondering if there was anything available within galaxy that would let you do the fo...
• Samtools Output
  Hello, I am having trouble replicating the great output you get after running samtools "Filter p...
• Dataset Not Appearing As Available Input To Sam Analyses
  Hi, I'm trying to use the SAM/Filter pileup analysis on some pileup output files I've uploaded. B...
• Need help with "Filter pileup" tool: not recognizing pileup data in "Select Dataset" popup menu
  I have been (roughly) following the tutorial on https://usegalaxy.org/u/aun1/p/mtdemo-getting-th...
• Pileup error: line length exceeds XXX in sequence YYY
  Hi,    I mapped my reads, filtered unpaired reads, converted to BAM and now I want to generate ...
• How To Extract Geneid From Pileup File?
  Dear galaxy-users, I am working on a project to identify and genotype SNPs in targeted genes. ...
• Freebayes coverage enquiry
  Silly question time: I have been using Freebayes to find variants in my data, using the simple s...
• IT PGM File type - every base position total coverage + alt allele coverage
  Hey everyone, To simplify my question: -I've sequenced a single sample Is there an Ion Torrent-...
• Genbank Submission - How To Generate Fasta (Not Fastq) Files
  I still haven't found an easy solution to this problem and I am afraid I'm going to have to write...
• Re: Assemble A Consensus Genome From Ngs Data
  Hi David, I'm sorry for a slow response. Relatively recently I solved a problem a bit like this a...
• pileup --position in galaxy
  How do I get samtools pileup to work only on a certain set of positions (say a BED file)?