Ultra deep sequencing validation

knights-lab / analysis_SHOGUN

Analysis scripts and code for reproducing the analysis for the SHOGUN paper

MIT License

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Ultra deep sequencing validation #9

Open bhillmann opened 7 years ago

bhillmann commented 7 years ago

[ ] Use an ultra-deep sequencing run to get rarefaction curve of imputed vs. observed genes
[x] Download the data

bhillmann commented 7 years ago

Ultra-deep sequencing should be downloaded

bhillmann commented 7 years ago

The path for this task is located below:

ultra_deep/

bhillmann commented 7 years ago

for i in `cat extract_files.txt`; do 7z -y x -so $i | 7z -y x -si -ttar -o./R1_QC; done 
shi7en -SE --combine_fasta False --convert_fasta False -trim_l 50 -i ./ -o ./R1_QC