Skip to content

StanfordBioinformatics/qualia

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

11 Commits
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

qualia

Scripts for preparation and processing of exome data

Procedure for copying data from encyrpted hard drives

  1. Plug in hard drive
  2. Enter passcode to unlock hard drive as described in Apricorn manual
  • Enter passcode
  • Press unlock button
  • The unlock padlock icon will turn green if entered correctly
  1. Run transfer script
~/src/qualia/bin/transfer_from_drive.py --hard_drive CLA123456

The transfer script will copy all data from from the hard drive using rsync to a predetermined location on a local computing cluster.

Unpacking compressed files and verifying checksums

  1. Log into computing cluster and move to copy destination
  2. Run the checksum verification script
~/src/qualia/bin/unpack_and_check.py

Any failures will be reported to the terminal. You can also check the logs for any files where the found checksum does not match the checksum reported in the manifest

grep FAILED checksum.log

This job can be run on the computing cluster like this:

qs -N "md5sum-check" -pe shm 8 "module load python/2.7; python /home/gmcinnes/src/ClaritasExomeAnalysis/bin/unpack_and_check.py"

Running FastQC on the cluster

for x in `cat sample_list.txt | grep bam | grep -v bai` ; do qs -N "fastqc" "module load fastqc; fastqc -o fastqc/CLA00127 -f bam $x" ; done

Unpack the results

cd fastqc/CLA00127
unzip *.zip

Rename data files and link them to single directory

for x in `ls | grep -v zip | grep -v html` ; do s=`echo $x | cut -f1 -d_` ; echo $s ; mv $x\_fastqc/fastqc_data.txt $x\_fastqc/$x.fastqc_data.txt; done
mkdir reports
ln -s SHIP*_fastqc/SHIP*.fastqc_data.txt reports

Run fastqc analysis script

Rscript ~/src/qualia/bin/fastqc_analysis.R --drive_id='CLA00127' --path='fastqc/CLA00127/reports'

About

Scripts for preparation and processing of exome data from Claritas

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published