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Galaxy docker image

git clone https://github.com/MingChen0919/docker-galaxy-dibbss.git
cd docker-galaxy-grreport-dibbs
docker build -t "docker-galaxy-grreport-dibbs" .
  • Start a container and launch galaxy
docker run -i -t -p 8080:80 -p 8021:21 -p 8022:22 \
  -e "GALAXY_CONFIG_ADMIN_USERS=example@gmail.com" \
  mingchen0919/docker-galaxy-grreport-dibbs \
  /bin/bash

## Launch galaxy
startup
  • Go to: http://127.0.0.1:8080/
  • Register an account with the email address: your_email@gmail.com, then you will have admin access.

Galaxy workflows schedule

RNA

  • (P01)Transcriptome assembly. May 1, 2016
    • Input: raw reads in fastq format
    • Tool: Trimmomatic -> Trinity
    • Output: fasta file
  • (P02)RNASeq alignment to a reference
    • Input: raw reads in fastq format
    • Input: reference genome
    • Input: reference annotation (gff3)
    • Tool: Trimmomatic -> Tophat
    • Output: bam file (either all in 1 file w/ RG or each lib in different file)
  • (P03)RNASeq Differential Expression analysis (Control vs Treatment with biological replicates). May 1, 2016
    • Input: bam file (either all in 1 file w/ RG or each lib in different file)
    • Tool: HTSeq -> DESeq2
    • Output: DESeq2 matrix file with p-values
  • (P04)RNASeq Variant discovery (against the reference). June 1, 2016 * Input: bam file (either all in 1 file w/ RG or each lib in different file) * Tool: mpileup -> samtools * Output: vcf * Downstream possible feature: deal with ploidy, SNPEff to determine impact of variation
  • (P05)RNASeq Variant discovery (between samples). June 1, 2016 * Input: bam file (either all in 1 file w/ RG or each lib in different file) * Tool: mpileup -> samtools -> need to investigate last step - can we use vcftools or custom script to filter results * Output: filtered vcf * Downstream possible feature: deal with ploidy, SNPEff to determine impact of variation
  • (P06)Gene co-expression network construction. July 1, 2016 (Talk to Miriam about this one) * Input: bam file (either all in 1 file w/ RG or each lib in different file) * Tool: htseq -> WGCNA * Output: network file?
  • (P07)MiRNA analysis. August 1, 2016 (Talk to Thomas about this one) * Input: raw reads in fastq format * Input: MIRBase gff3 for organism (if available) * Tool: trimmomatic (stringent length filter and adapter) -> compare to MIRBase -> determine known/unknown miRNA loci * Output: raw counts of known miRNAs by library * Downstream possible feature: map to reference and discover novel elements, normalize counts * MiRDeep2      * Public galaxy server for miRNA analysis: http://cefap.icb.usp.br/galaxy/

DNA

  • (P08)DNASeq Re-sequencing alignment. September 1, 2016
    • Input: raw reads in fastq format
    • Input: reference genome
    • Tool: Trimmomatic -> Bowtie2
    • Output: bam file (either all in 1 file w/ RG or each lib in different file)
  • (P09)DNASeq Variant discovery (against the reference). October 1, 2016 * Input: bam file (either all in 1 file w/ RG or each lib in different file) * Tool: mpileup -> samtools * Output: vcf * Downstream possible feature: deal with ploidy, SNPEff to determine impact of variation
  • (P10)DNASeq Variant discovery (between samples). October 1, 2016 * Input: bam file (either all in 1 file w/ RG or each lib in different file) * Tool: mpileup -> samtools -> need to investigate last step - can we use vcftools or custom script to filter results * Output: filtered vcf * Downstream possible feature: deal with ploidy, SNPEff to determine impact of variation
  • (P11)Prediction of functional genetic variants (SNPEff or annovar). November 1, 2016