Add new script

additional_analyses/HMP_gene_catalog/count_IMP_HMP.sh

+#!/bin/bash -l
+
+
+declare -a SAMPLES=("HF1" "HF2" "HF3" "HF4" "HF5")
+
+for S in "${SAMPLES[@]}" 
+do 
+
+IMP_MG_BAM="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/${S}/Assembly/MG.reads.sorted.bam"
+IMP_MG_MEGAHIT_BAM="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/${S}_megahit/Assembly/MG.reads.sorted.bam"
+IGC_MG_BAM="/scratch/users/snarayanasamy/IMP_MS_data/HMP_IGC_mapping/${S}/MG_IMP_x_HMP.sorted.bam"
+IMP_MT_BAM="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/${S}/Assembly/MT.reads.sorted.bam"
+IMP_MT_MEGAHIT_BAM="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/${S}_megahit/Assembly/MT.reads.sorted.bam"
+IGC_MT_BAM="/scratch/users/snarayanasamy/IMP_MS_data/HMP_IGC_mapping/${S}/MT_IMP_x_HMP.sorted.bam"
+
+echo "IGC and IMP MG total reads"
+sort <(samtools view -f 2 $IMP_MG_BAM | cut -f1) <(samtools view -f 2 $IGC_MG_BAM | cut -f1) | uniq | wc -l
+
+echo "IGC and IMP-megahit MG total reads"
+sort <(samtools view -f 2 $IMP_MG_MEGAHIT_BAM | cut -f1) <(samtools view -f 2 $IGC_MG_MEGAHIT_BAM | cut -f1) | uniq | wc -l
+
+echo "IGC and IMP MT total reads"
+sort <(samtools view -f 2 $IMP_MT_BAM | cut -f1) <(samtools view -f 2 $IGC_MT_BAM | cut -f1) | uniq | wc -l
+
+echo "IGC and IMP-megahit MT total reads"
+sort <(samtools view -f 2 $IMP_MT_MEGAHIT_BAM | cut -f1) <(samtools view -f 2 $IGC_MT_MEGAHIT_BAM | cut -f1) | uniq | wc -l
+
+done