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Intro to the Command Line

Joe Fass

[email protected]

Multi-line commands from slides:

wget --no-check-certificate ftp://igenome:[email protected]/PhiX/Illumina/RTA/PhiX_Illumina_RTA.tar.gz
curl -k https://bioshare.bioinformatics.ucdavis.edu/bioshare/download/pdhqicmfgw2bra8/variant.neighborhoods.fa > regions.fa

grep ">" regions.fa | cut -c 2-
grep ">" regions.fa | cut -c 2- | cut -f1 -d:
grep ">" regions.fa | cut -c 2- | cut -f1 -d: | sort
grep ">" regions.fa | cut -c 2- | cut -f1 -d: | sort | uniq -c
grep ">" regions.fa | cut -c 2- | cut -f1 -d: | sort | uniq -c | sort -rn -k1,1

ln -s PhiX/Illumina/RTA/Sequence/WholeGenomeFasta/genome.fa .

bwa mem genome.fa regions.fa 1> aln.sam 2> aln.err

grep ">" regions.fa | cut -c2- | while read header; do echo "contig_$header" >> b; done