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tf_binding.sh.save
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tf_binding.sh.save
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#!/bin/bash
#PBS -q hotel
##PBS -N tf_binding.sh
#PBS -l nodes=10:ppn=2
#PBS -l walltime=0:50:00
#PBS -o tf_binding.sh.o
#PBS -e ef_binding.sh.e
#PBS -V
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#PBS -M [email protected]
#PBS -m abe
#PBS -A e1luo
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#cd /oasis/tscc/scratch/e1luo
#mpirun -v -machinefile $PBS_NODEFILE -np 20 <./mpi.out>
cd /home/ecwheele/biom262/code/biom262-2016/weeks/week01/data
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cd ~/code/biom262-2016/weeks/week01/data
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awk -F "\t" '{if($3 == "transcript") {print $0}}' gencode.v19.annotation.chr22.gtf > gencode.v19.annotation.chr22.transcript.gtf
#EXERCISE3 (include loading of biotools)
bedtools intersect -a gencode.v19.annotation.chr22.transcript.promoter.gtf -b tf.nfkb.bed > gencode.v19.annotation.chr22.transcript.promoter.nfkb.gtf
bedtools getfasta -fi GRCh37.p13.chr22.fa -bed gencode.v19.annotation.chr22.transcript.promoter.nfkb.gtf -fo gencode.v19.annotation.chr22.transcript.promoter.nfkb.fasta
#Exercise 4: Use bedtools intersect to overlap TFs with promoter
bedtools intersect -a gencode.v19.annotation.chr22.transcript.promoter.gtf -b tf.nfkb.bed > gencode.v19.annotation.chr22.transcript.promoter.nfkb.gtf
#Exercise 5: Use bedtools getfasta to extract sequences
bedtools getfasta -fi GRCh37.p13.chr22.fa -bed gencode.v19.annotation.chr22.transcript.promoter.nfkb.gtf -s -fo gencode.v19.annotation.chr22.transcript.promoter.nfkb.fasta
#EXERCISE6
echo "Hello I am a message in standard out (stdout)"