From e0c9bb58dacdb64b6e5e9ffe568346c3fb79b2d1 Mon Sep 17 00:00:00 2001 From: pratas <6882743+pratas@users.noreply.github.com> Date: Wed, 4 Jan 2023 10:50:12 +0000 Subject: [PATCH] mode and sh --- benchmark/comparison.sh | 23 ----------------------- 1 file changed, 23 deletions(-) delete mode 100644 benchmark/comparison.sh diff --git a/benchmark/comparison.sh b/benchmark/comparison.sh deleted file mode 100644 index e7cd739..0000000 --- a/benchmark/comparison.sh +++ /dev/null @@ -1,23 +0,0 @@ -#!/bin/bash -# -# conda install -c bioconda bedtools=2.29.2 -y -# where is geecee? -# -module load Tools/BEDTools/2.29.2 -# -bedtools intersect -f 1 -a hap1.alcor.bed -b TME204_HiFi_HiC_allmap.hap1.chr.fasta.out.gff -wa > hap1_alcor_full_overlap.bed -bedtools intersect -a hap1.alcor.bed -b TME204_HiFi_HiC_allmap.hap1.chr.fasta.out.gff -v > hap1_alcor_unique.bed -bedtools intersect -a TME204_HiFi_HiC_allmap.hap1.chr.fasta.out.gff -b hap1.alcor.bed -v > hap1_repeatmasker_unique.bed -bedtools getfasta -fi TME204_HiFi_HiC_allmap.hap1.fasta.masked -bed hap1_alcor_unique.bed > hap1_alcor_unique.fa -/usr/local/ngseq/packages/Tools/EMBOSS/6.6.0/bin/geecee hap1_alcor_unique.fa hap1_alcor_unique.gc.txt -perl fas_getlen.pl hap1_alcor_unique.fa > hap1_alcor_unique.len.txt -# -bedtools intersect -f 1 -a hap2.alcor.bed -b TME204_HiFi_HiC_allmap.hap2.chr.fasta.out.gff -wa > hap2_alcor_full_overlap.bed -bedtools intersect -a hap2.alcor.bed -b TME204_HiFi_HiC_allmap.hap2.chr.fasta.out.gff -v > hap2_alcor_unique.bed -bedtools intersect -a TME204_HiFi_HiC_allmap.hap2.chr.fasta.out.gff -b hap2.alcor.bed -v > hap2_repeatmasker_unique.bed -bedtools getfasta -fi TME204_HiFi_HiC_allmap.hap2.fasta.masked -bed hap2_alcor_unique.bed > hap2_alcor_unique.fa -/usr/local/ngseq/packages/Tools/EMBOSS/6.6.0/bin/geecee hap2_alcor_unique.fa hap2_alcor_unique.gc.txt -perl fas_getlen.pl hap2_alcor_unique.fa > hap2_alcor_unique.len.txt -# -perl repeatmasker_count_missing.pl TME204_HiFi_HiC_allmap.hap1.chr.fasta.out.gff hap1_repeatmasker_unique.bed -perl repeatmasker_count_missing.pl TME204_HiFi_HiC_allmap.hap2.chr.fasta.out.gff hap2_repeatmasker_unique.bed