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RSeQC-Tutorial-[optional].md

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RSeQC

Background: RSeQC is a tool that can be used to generate QC reports for RNA-seq. For more information, please check: Tool Homepage

Objectives: In this section, we will try to generate a QC report for a data set downloaded from RSeQC website.

Files needed:

  • Aligned bam file.
  • Index file for the aligned bam.
  • A RefSeq bed file.

#Copy RSeQC Data

set your working directory and copy the necessary files

  mkdir -p ~/workspace/rnaseq/
  cp -r ~/CourseData/RNA_data/RSeQC/RSeQC.zip ~/workspace/rnaseq/
  cd ~/workspace/rnaseq/

#Unzip the RSeQC file unzip RSeQC.zip cd RSeQC/ Note: You should now see the bam, index, and RefSeq bed files listed

#Run RSeQC commands: bam_stat.py -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam clipping_profile.py -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o tutorial geneBody_coverage.py -r hg19_RefSeq.bed -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o tutorial infer_experiment.py -r hg19_RefSeq.bed -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam inner_distance.py -r hg19_RefSeq.bed -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o tutorial junction_annotation.py -r hg19_RefSeq.bed -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o tutorial junction_saturation.py -r hg19_RefSeq.bed -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o tutorial read_distribution.py -r hg19_RefSeq.bed -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam read_duplication.py -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o tutorial read_GC.py -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o tutorial read_NVC.py -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o tutorial read_quality.py -i Pairend_nonStrandSpecific_36mer_Human_hg19.bam -o tutorial

#Go through the generated PDFs ls *.pdf