Similar posts • Search »

• Varscan and pileup files
  Hi, I would like to perform a variant calling analysis using Varscan and I used Generate pileup ...
• empty QUAL field
  Hi, I'm trying to analyze polymorphic sites in the individual. After running Naive Variant Calle...
• Varscan on multiple samples generates error
  Hello, I am using "samtools mpileup" to generate a pileup file from my .bam dataset and then pas...
• Combining FASTA and Qual files to generate FASTQ
  I am trying to combine a .FASTA file with a .QUAL file using the tool provided under "NGS: QC and...
• empty QUAL filed in Naive Variant caller vcf output
  Hi, The QUAL field in vcf output of Naive Variant Caller is empty for all the variants. Any reas...
• VarScan on Galaxy
  Hi All ive been trying to use varsacn on my pileup file in Galaxy  in the results, i get "N" in...
• To varscan mpileup data
  HI, I have run the mpileup (process is completed and successful), and was trying to analyse the p...
• Filter Varscan VCF
  Hello, I have a VCF file obtained from the Varscan tool. I want to filter the variants based on ...
• Need help with "Varscan" tool
  In my browser window, Varscan for variant detection does not allow me to add datasets. What is wr...
• How do I process multiple pileup files at once with Varscan to get the vcf files?
  I have a list of 100 SRA IDs for which I need to get the VCF files using VARSCAN. VARSCAN takes...
• multiplex primer design...Help!
  Hi I'm trying to design a suite of 10-15 microsat primers using NGS. I have the raw output files...
• How do I determine the correct filtering threshold in VCFfilter after running FreeBayes
  I would like to perform a VCFfilter on my FreeBayes data but I'm not sure how to choose the corre...
• Bowtie with -a --best --strata does not seem to limit alignments to the best strata
  I am using bowtie for illumina on the NGS Galaxy public server. This is the code for the run tha...
• This job was terminated because it used more memory than it was allocated (new post)
  To Galaxy, I've read on this forum about the proposed solutions to this memory issue. Other than...
• Running SnpEff on Galaxy
  Hello, I would like to annotate a .vcf file and also summarize possible effects variants can hav...
• How to run a workflow using Dataset Collection?
  HI, I created a workflow which has as input a dataset collection which consists of 12 BAM Files....
• Convert fna/.qual files to .fastq
  I have 454 .fna and .qual files that I would like to convert to fastq format. It appears that onl...
• TopHat Error Occurred with Dataset
  Hello!  I am attempting to map solid colorspace data with galaxy.  I am running the pipeline as f...