Welcome to PSMC Tutorial!

Note

I request you ALL to type in all the code rather than copying from the tutorial. You will get better at coding and understand the code better.

Contents

• Installation of required softwares
  • 1) FastQC
  • 2) Trimmomatic
  • 3) Burrows-Wheeler Aligner
  • 4) Samtools and htslib suit
  • 5) Picard Tools
  • 6) Bioawk
  • 7) BCFTools
  • 8) PSMC
  • 9) R and R-Studio
• Data pre-processing steps for PSMC
  • A) Download Data for Jungle Owlet
  • B) Check the QC of your RAW file
  • C) Trim the RAW files using Trimmomatic
  • D) Get the reference genome
  • E) Map the trimmed data to a reference
  • F) Filter the mapped data (Quality, Sort, PCR Duplicates removal)
  • G) BAMQC
  • H) Identifying sex linked chromosome
  • I) Retain data mapping only to Autosomal chromosomes from the reference.
  • J) Creating consensus fq file
• Alright, Let’s run the actual things - PSMC
  • A) Initial runs
  • B) Bootstrapping PSMC
  • C) Final text output
• Ploting the PSMC results using R