Find allele (e.g., SNPs) specific effects

hpcf_interactive

module load conda3

source activate /home/yli11/.conda/envs/gkmSVM

Rscript run_gkmSVM.R ctcfpos.bed hg18 nr10mers.fa ref.fa alt.fa

run_gkmSVM.R H2_ATAC.bed hg19 ~/HemTools/share/misc/nr10mers.fa ../ref.fa ../alt.fa

=cut delta 1

inputFile=input

ncore=1
mem=16000

module load conda3
source activate gkmSVM

dir=${COL1}
cd $dir
file=`ls *Peak`
input=${file%.narrowPeak}.input.bed
sort -k 8gr $file | head -n 20000 | awk -F "\t" '{print $1"\t"$2"\t"$3}' > $input
run_gkmSVM.R $input hg19 ~/HemTools/share/misc/nr10mers.fa ../ref.fa ../alt.fa

=cut email 2 all

module load python/2.7.13

send_email_v1.py -m "deltaSVM is finished!" -j "deltaSVM"

code @ github.