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Commit f224ad47 authored by Shaman Narayanasamy's avatar Shaman Narayanasamy
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Correction

parent 0f74906f
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additional_analyses/HMP_gene_catalog/count_IMP_HMP.sh
View file @ f224ad47
......@@ -16,12 +16,12 @@ IMP_MT_BAM="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/${S}/Assembly/
IMP_MT_MEGAHIT_BAM="/scratch/users/snarayanasamy/IMP_MS_data/IMP_analysis/${S}_megahit/Assembly/MT.reads.sorted.bam"
IGC_MT_BAM="/scratch/users/snarayanasamy/IMP_MS_data/HMP_IGC_mapping/${S}/MT_IMP_x_HMP.sorted.bam"
paste <(echo -e "${S}_MG_IMP_IGC\t") <(sort <(samtools view -f 2 -@ ${THREADS} ${IMP_MG_BAM} | cut -f1) <(samtools view -f 2 -@ ${THREADS} ${IGC_MG_BAM} | cut -f1) | uniq | wc -l) >> IMP2IGC_mapping.txt
paste <(echo -e "${S}_MG_IMP_IGC") <(sort <(samtools view -f 2 -@ ${THREADS} ${IMP_MG_BAM} | cut -f1) <(samtools view -f 2 -@ ${THREADS} ${IGC_MG_BAM} | cut -f1) | uniq | wc -l) > IMP2IGC_mapping.txt
paste <(echo -e "${S}_MG_IMP-megahit_IGC\t") <(sort <(samtools view -f 2 -@ ${THREADS} ${IMP_MG_MEGAHIT_BAM} | cut -f1) <(samtools view -f 2 -@ ${THREADS} ${IGC_MG_BAM} | cut -f1) | uniq | wc -l) >> IMP2IGC_mapping.txt
paste <(echo -e "${S}_MG_IMP-megahit_IGC") <(sort <(samtools view -f 2 -@ ${THREADS} ${IMP_MG_MEGAHIT_BAM} | cut -f1) <(samtools view -f 2 -@ ${THREADS} ${IGC_MG_BAM} | cut -f1) | uniq | wc -l) >> IMP2IGC_mapping.txt
<(echo -e "${S}_MT_IMP_IGC\t") <(sort <(samtools view -f 2 -@ ${THREADS} ${IMP_MT_BAM} | cut -f1) <(samtools view -f 2 -@ ${THREADS} ${IGC_MT_BAM} | cut -f1) | uniq | wc -l) >> IMP2IGC_mapping.txt
paste <(echo -e "${S}_MT_IMP_IGC") <(sort <(samtools view -f 2 -@ ${THREADS} ${IMP_MT_BAM} | cut -f1) <(samtools view -f 2 -@ ${THREADS} ${IGC_MT_BAM} | cut -f1) | uniq | wc -l) >> IMP2IGC_mapping.txt
paste <(echo -e "${S}_MT_IMP-megahit_IGC\t") <(sort <(samtools view -f 2 -@ ${THREADS} ${IMP_MT_MEGAHIT_BAM} | cut -f1) <(samtools view -f 2 -@ ${THREADS} ${IGC_MT_BAM} | cut -f1) | uniq | wc -l) >> IMP2IGC_mapping.txt
paste <(echo -e "${S}_MT_IMP-megahit_IGC") <(sort <(samtools view -f 2 -@ ${THREADS} ${IMP_MT_MEGAHIT_BAM} | cut -f1) <(samtools view -f 2 -@ ${THREADS} ${IGC_MT_BAM} | cut -f1) | uniq | wc -l) >> IMP2IGC_mapping.txt
done
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