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script_map.sh
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16 lines (8 loc) · 1.13 KB
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#!/bin/bash
module load bwa
# bwa mem -t 10 -R '@RG\tID:Unknwn\tPL:Illumina\tLB:library\tSM:' -M ../Map/Zea_mays.AGPv4.dna.toplevel.fa ../SRR3134441_1_paired.fastq ../SRR3134441_1_reverse_paired.fastq > SRR3134441_trim.sam
# bwa mem -t 10 -R '@RG\tID:Unknwn\tPL:Illumina\tLB:library\tSM:' -M ../Map/Zea_mays.AGPv4.dna.toplevel.fa ../SRR3134467_1_paired.fastq ../SRR3134467_1_reverse_paired.fastq > SRR3134467_trim.sam
# bwa mem -t 10 -R '@RG\tID:Unknwn\tPL:Illumina\tLB:library\tSM:' -M ../Map/Zea_mays.AGPv4.dna.toplevel.fa ../SRR3134468_1_paired.fastq ../SRR3134468_1_reverse_paired.fastq > SRR3134468_trim.sam
bwa mem -t 10 -R '@RG\tID:Unknwn\tPL:Illumina\tLB:library\tSM:' -M ../Map/Zea_mays.AGPv4.dna.toplevel.fa ../SRR3134441_1.fastq.gz ../SRR3134441_2.fastq.gz > SRR3134441_untrim.sam
bwa mem -t 10 -R '@RG\tID:Unknwn\tPL:Illumina\tLB:library\tSM:' -M ../Map/Zea_mays.AGPv4.dna.toplevel.fa ../SRR3134468_1.fastq.gz ../SRR3134468_2.fastq.gz > SRR3134468_untrim.sam
bwa mem -t 10 -R '@RG\tID:Unknwn\tPL:Illumina\tLB:library\tSM:' -M ../Map/Zea_mays.AGPv4.dna.toplevel.fa ../SRR3134467_1.fastq.gz ../SRR3134467_2.fastq.gz > SRR3134467_untrim.sam