NSCI 580A4 fall 2017

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#NAME: Erin Nishimura
#
#DATE: August 31, 2017
#
#ASSIGNMENT: 2
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1) wc S288C_reference_sequence_R64-1-1_20110203.fsa

2) wc -l S288C_reference_sequence_R64-1-1_20110203.fsa

3) grep '>' S288C_reference_sequence_R64-1-1_20110203.fsa | wc
OR
grep '>' S288C_reference_sequence_R64-1-1_20110203.fsa | wc - l
OR
grep -c '>' S288C_reference_sequence_R64-1-1_20110203.fsa

4) head -n 1000 S288C_reference_sequence_R64-1-1_20110203.fsa > test.fsa
OR
head 1000 S288C_reference_sequence_R64-1-1_20110203.fsa > test.fsa

5) grep '^chr' saccharomyces_cerevisiae_R64-1-1_20110208.gff > sacCer3_tab.gff
OR
grep ^chr saccharomyces_cerevisiae_R64-1-1_20110208.gff > sacCer3_tab.gff

6) grep '\ttRNA\t' sacCer3_tab.gff > sacCer3_tRNA.gff
OR
grep -P '\ttRNA\t' sacCer3_tab.gff > sacCer3_tRNA.gff
OR
grep $'\ttRNA\t' sacCer3_tab.gff > sacCer3_tRNA.gff

7) cut -f 3 sacCer3_tRNA.gff | sort | uniq

8) cut -f 1,4,5,7 sacCer3_tRNA.gff > sacCer3_tRNA.bed

9A) 5
9B) 48
9C) 240

10)
#SBATCH –partition=sgpu
#SBATCH –nodes=1
#SBATCH –ntasks=24
#SBATCH –time=24:00:00
#SBATCH –qos=normal

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