BWA mapping workflow

$ cd hypoxia_CheckM/final_bins2
$ for i in *.fasta; do name=`echo $i | awk 'BEGIN{FS="."}{print $1}'`; echo ">"$name >> allbins_concat.fa; grep -v '>' $i >> allbins_concat.fa; done

$ bwa index allbins_concat.fa

$ for i in D1 D2 D3 E2 E2A E4; do ./multi_q_bwa $i; done
$ for i in D1 D2 D3 E2 E2A E4; do ./multi_q_bwa2 $i; done

-------------------------------
RNA
$ cat multi_q_bwa

#!/bin/bash
# specify stdin
file=$1
cat <<EOF > tmp.$$

#!/bin/bash
#PBS -q checkpt
#PBS -A hpc_compgen04
#PBS -l nodes=1:ppn=16
#PBS -l walltime=10:00:00
#PBS -o /project/jcthrash/thrashc/hypoxia
#PBS -j oe
#PBS -N bwa.$file

date
cd /project/jcthrash/thrashc/hypoxia/
bwa aln -t 16 allbins_concat.fa Project_Mason_Thrash_metatranscriptomes/Sample_$file/*_RNA_combined_trimmed.fastq > supercontig.$file.RNA.aln.sai
bwa samse allbins_concat.fa supercontig.$file.RNA.aln.sai Project_Mason_Thrash_metatranscriptomes/Sample_$file/*_RNA_combined_trimmed.fastq > supercontig.$file.RNA.aln.sam
samtools view -@ 16 -bS -o supercontig.$file.RNA.aln.bam supercontig.$file.RNA.aln.sam
samtools sort -@ 16 supercontig.$file.RNA.aln.bam supercontig.$file.RNA.aln.sorted
samtools index supercontig.$file.RNA.aln.sorted.bam
samtools idxstats supercontig.$file.RNA.aln.sorted.bam > supercontig.$file.RNA.aln.stats
date

exit 0
EOF

qsub tmp.$$
exit 0

-------------------------------
DNA
$ cat multi_q_bwa2

#!/bin/bash
# specify stdin
file=$1
cat <<EOF > tmp.$$

#!/bin/bash
#PBS -q checkpt
#PBS -A hpc_compgen04
#PBS -l nodes=1:ppn=16
#PBS -l walltime=10:00:00
#PBS -o /project/jcthrash/thrashc/hypoxia
#PBS -j oe
#PBS -N bwa.$file

date
cd /project/jcthrash/thrashc/hypoxia/
bwa aln -t 16 allbins_concat.fa Project_Mason_Thrash_Metagenomes/Combined_Assembly/$file.combined_trimmed.fastq > supercontig.$file.DNA.aln.sai
bwa samse allbins_concat.fa supercontig.$file.DNA.aln.sai Project_Mason_Thrash_Metagenomes/Combined_Assembly/$file.combined_trimmed.fastq > supercontig.$file.DNA.aln.sam
samtools view -@ 16 -bS -o supercontig.$file.DNA.aln.bam supercontig.$file.DNA.aln.sam
samtools sort -@ 16 supercontig.$file.DNA.aln.bam supercontig.$file.DNA.aln.sorted
samtools index supercontig.$file.DNA.aln.sorted.bam
samtools idxstats supercontig.$file.DNA.aln.sorted.bam > supercontig.$file.DNA.aln.stats

date

exit 0
EOF

qsub tmp.$$
exit 0
-------------------------------