GBS722 2013: Difference between revisions

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== Ref-based Protocol ==
== Ref-based Protocol ==
# '''QC''': Demo Tools > FastQC (4x)
# '''For each sample (2x)'''
# '''Mapping (2x)''':  
## '''QC''': Demo Tools > FastQC (2x: forward & reverse reads)
## Demo Tools > BWA for Illumina (ref from history, paired end)
## '''Mapping''':  
## SAM Tools > SAM-to-BAM (ref from history)
### Demo Tools > BWA for Illumina (ref from history, paired end)
## rename & download .bam & .bai for IGV visualization
### SAM Tools > SAM-to-BAM (ref from history)
# '''QC''': SAM Tools > Flag Stat  
### rename & download .bam & .bai for IGV visualization
# '''SNP calling''': NGS: SAM Tools > Generate VCF with mpileup piped through bcftools view
### '''QC''': SAM Tools > Flag Stat  
# '''SNP assessment''': Demo Tools > SnpEff (Vaccinia_Western_Reserve (vacwr.NC_006998.1))
## '''SNP calling''': NGS: SAM Tools > Generate VCF with mpileup piped through bcftools view (ref from history)
## '''SNP assessment''': Demo Tools > SnpEff (output=VCF; ref=Vaccinia_Western_Reserve (vacwr.NC_006998.1), up/down=200 bases, filter=select_all)
# '''Compare Genomes''': Join, Subtract and Group > Compare two Datasets (columns 1-5)
# '''Compare Genomes''': Join, Subtract and Group > Compare two Datasets (columns 1-5)
Workflow for this protocol: (import to use)
* Shared Data > Workflows >  GBS722 VACV-WR 125k - sample BWA to ref in hist
* https://galaxy.uabgrid.uab.edu/u/curtish/w/gbs722-vacv-wr-125k---sample-sample-to-ref
Example History:
* https://galaxy.uabgrid.uab.edu/u/curtish/h/gbs722-vacv-wr-125k---sample-bwa-to-ref-in-history


== Denovo Protocol (2x) ==
== Denovo Protocol (2x) ==
# '''Denovo contigs ''':  
# '''Denovo contigs ''':  
## NGS: Assembly > velveth (shortPairedRead & shortPairedRead2)
## NGS: Assembly > velveth (k=29, format=fast'''q''', shortPairedRead & shortPairedRead2)
## NGS: Assembly > velvetg (MinContigLen=200, UsePairedReads=250)
## NGS: Assembly > velvetg (MinContigLen=200, UsePairedReads=250)
# '''Map Contigs to Ref''':  
# '''Map Contigs to Ref''':  
## Demo Tools > BWA SW for Contigs
## Demo Tools > BWA SW for Contigs (ref from history)
## SAM Tools > SAM-to-BAM
## SAM Tools > SAM-to-BAM (ref from history)
## rename & download .bam & .bai for IGV visualization
## rename & download .bam & .bai for IGV visualization
# '''NCBI Blast un-mapped contigs''': http://ncbi.nlm.nih.gov > [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome nucleotide blast megablast]
## '''QC''':
### SAM Tools > flagstat
### BWA_SW SAM un-mapped contigs:  
#### http://ncbi.nlm.nih.gov > [http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&BLAST_PROGRAMS=megaBlast&PAGE_TYPE=BlastSearch&SHOW_DEFAULTS=on&LINK_LOC=blasthome nucleotide blast megablast]
 
Workflow for this protocol: (import to use)
* Shared Data > Workflows >  GBS722 VACV-WR 125k - sample denovo with BWASW to ref in hist
* https://galaxy.uabgrid.uab.edu/u/curtish/w/gbs722-vacv-wr-125k---sample-denovo-with-bwasw-to-ref-in-hist
Example History:
* https://galaxy.uabgrid.uab.edu/u/curtish/h/gbs722-vacv-wr-125k---sample-bwa-to-ref-in-history


== Recommended Visualization ==
== Recommended Visualization ==

Latest revision as of 18:43, 14 March 2013

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