GBS722 2013

From Cheaha
Jump to navigation Jump to search


Attention: Research Computing Documentation has Moved
https://docs.rc.uab.edu/


Please use the new documentation url https://docs.rc.uab.edu/ for all Research Computing documentation needs.


As a result of this move, we have deprecated use of this wiki for documentation. We are providing read-only access to the content to facilitate migration of bookmarks and to serve as an historical record. All content updates should be made at the new documentation site. The original wiki will not receive further updates.

Thank you,

The Research Computing Team

VACV-WR WT vs DRUG protocol in Galaxy

This is an abbreviated protocol cheat-sheet to help students through the class exercises.

Links

UAB Galaxy - https://galaxy.uabgrid.uab.edu

Ref Genome @ NCBI

Reads in UAB Galaxy

IGV Setup

  1. JNLP launch: http://www.broadinstitute.org/software/igv/download
  2. Create VACV-WR genome
    1. Genomes > Create .genome
      • Menu: Genomes > Create .genome file
      • Unique Identifier: NC_006998.1
      • Descriptive Name: VACV-WR
      • FASTA File: NC_006998.fna
      • Gene File: NC_006998.gff

Ref-based Protocol

  1. For each sample (2x)
    1. QC: Demo Tools > FastQC (2x: forward & reverse reads)
    2. Mapping:
      1. Demo Tools > BWA for Illumina (ref from history, paired end)
      2. SAM Tools > SAM-to-BAM (ref from history)
      3. rename & download .bam & .bai for IGV visualization
      4. QC: SAM Tools > Flag Stat
    3. SNP calling: NGS: SAM Tools > Generate VCF with mpileup piped through bcftools view (ref from history)
    4. SNP assessment: Demo Tools > SnpEff (output=VCF; ref=Vaccinia_Western_Reserve (vacwr.NC_006998.1), up/down=200 bases, filter=select_all)
  2. Compare Genomes: Join, Subtract and Group > Compare two Datasets (columns 1-5)

Workflow for this protocol: (import to use)

Example History:

Denovo Protocol (2x)

  1. Denovo contigs :
    1. NGS: Assembly > velveth (k=29, format=fastq, shortPairedRead & shortPairedRead2)
    2. NGS: Assembly > velvetg (MinContigLen=200, UsePairedReads=250)
  2. Map Contigs to Ref:
    1. Demo Tools > BWA SW for Contigs (ref from history)
    2. SAM Tools > SAM-to-BAM (ref from history)
    3. rename & download .bam & .bai for IGV visualization
    4. QC:
      1. SAM Tools > flagstat
      2. BWA_SW SAM un-mapped contigs:
        1. http://ncbi.nlm.nih.gov > nucleotide blast megablast

Workflow for this protocol: (import to use)

Example History:

Recommended Visualization

  1. IGV, load tracks
    1. WT BWA_BAM
    2. Drug BWA_BAM
    3. WT Velvet_BWASW_BAM
    4. Drug Velvet_BWASW_BAM
Retrieved from "https://docs.uabgrid.uab.edu/w/index.php?title=GBS722_2013&oldid=4463"