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• High-Throughput "Proteomics" Pipeline?
  Hi BioStar, As we know the developement of high-throughput pipeline in different research field....
• How to specify pipelines(muse, mutect,...) in TCGAbiolinks when you want to use hg19?
  Dear all, I am trying to use different mutation analysis pipelines(muse, mutect for my tumor sam...
• ENCODE ATAC-seq pipeline peak calling
  I am looking at the ENCODE ATAC-seq pipeline: https://www.encodeproject.org/pipelines/ENCPL035XIO...
• Cdc Pipeline
  Has the CDC published a paper on their genome pipeline? I am curious to see what they are using.
• Use of OrthoFinder pipeline
  Hi, I am trying to use the OrthoFinder pipeline for prediction of orthologous groups among my set...
• Fred's metabarcoding pipeline : Build the OTU table / keyerror in python script
  Hello, I am using Frédéric Mahé's metabarcoding pipeline at: https://github.com/frederic-mahe/swa...
• Running IsoSeq pipeline
  I am analyzing Pacbio data for the first time and I have the following files 1) ..fastq.gz ...
• multi species_gene name to description
  Dear colleagues, I have a large set of gene names that belong to the "multiple species". I am w...
• How to set AWS_BATCH_JOB_ATTEMPT value when using curl to submit cromwell jobs to batch?
  I want to set AWS_BATCH_JOB_ATTEMPT in my pipeline. My pipeline is a cromwell wdl pipeline which ...
• How to validate the SNP calling pipeline?
  How to validate the SNP calling pipeline. I am looking for SNP calling validation methodologies.
• How to create 1000G_phase1.snps.high_confidence.hg19.sites.vcf ?
  Hi, i am new to bioinformatics. Wondering how "1000G_phase1.snps.high_confidence.hg19.sites.vcf" ...
• ribosomal RNA sorting by "SortmeRNA"
  When I am trying to sorting rRNA (Planarian transcriptome) using SortmeRNA on cluster after a few...
• GTEX RNA Seq. Pipeline
  Dear all, This is my first post here and I am hoping you can help me. I am currently doing a R...
• Need: Working Workflow Pipeline For Agilent Mirna Analysis Using Agimicrorna
  I am trying to use "AgiMicroRna" package for agilent miRNA analysis. I tried using the workflow...
• Galaxy DE lncRNA analysis pipeline
  Hi, I am trying to identify differentially expressed lncRNAs in tumor samples (18 replicates) com...
• Difference Between "Pipeline" And "Workflow" ?
  A quick and basic question today. I often see in literature (in particular in the context of NGS)...
• ddRAD analysis pipelines
  I have a Fish ddRAD data, 50 samples. In dDocent I am getting very low alignment ~30%. In ST...
• Error: could not find function "assay"and "assays "
  I am doing the pipeline according toturial. library(TCGAbiolinks) library(SummarizedExpe...