Metacentrum log in

  1. Log in to the metacentrum using your terminal. Please use skirit frontend.
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ssh -X user@skirit.ics.muni.cz
  1. Computing on frontend is forbidden, so ask for an interactive job with qsub. Specify the resources: 2CPU, 4GB RAM, scratch of 10GB and 2 hours.
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qsub -I -l select=1:ncpus=2:mem=4gb:scratch_local=10gb -l walltime=2:00:00
  1. Create a directory 'QC' to store your data. And go inside that directory.
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mkdir QC
cd QC
  1. Copy the folder from '/auto/brno2/home/bartonv/QC_example/example', to your own directory. Find out the structure of that folder. Where is the sequencing files located?
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cp -r /auto/brno2/home/bartonv/QC_example/example example
cd example
ls -R
  1. You can use file explorer (nautilus). Try to log in on frontend through sftp:// protocol.
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sftp://user@skirit.ics.muni.cz
  1. Check if fastqc module is available and load it.
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module avail fastqc
module load fastqc
  1. Display fastqc manual.
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fastqc -h
  1. Run fastqc on your data.
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fastqc *.fastq.gz
  1. Run multiqc on a folder where fastqc reports is. Check the output.
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module add python27-modules-gcc
multiqc .
  1. Run fastp (https://github.com/OpenGene/fastp), there is a module for that. And check quality again.