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insertsize.sh
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insertsize.sh
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cd ~/build/EMIRGE
for name in EA103N EA124N EA126N EA13N EA22N EA2N EA30N EA31N EA37N EA50N EA58N EA59N EA70N EA84N EA90N EA91N
#do
# sh bwa.sh EA_inbred $name
#done
cp /media/backup_2tb/Data/FlyMicrobiome/nonDrosophila/Round5/$1/$2_R1_unmapped.fq.gz $2_R1_nonDrosophila.fq.gz
cat /media/backup_2tb/Data/FlyMicrobiome/Wolbachia/$1/$2_Wolbachia_R1.fq.gz >> $2_R1_nonDrosophila.fq.gz
cp /media/backup_2tb/Data/FlyMicrobiome/nonDrosophila/Round5/$1/$2_R2_unmapped.fq.gz $2_R2_nonDrosophila.fq.gz
cat /media/backup_2tb/Data/FlyMicrobiome/Wolbachia/$1/$2_Wolbachia_R2.fq.gz >> $2_R2_nonDrosophila.fq.gz
gunzip $2_R2_nonDrosophila.fq.gz
./emirge.py $2 -1 $2_R1_nonDrosophila.fq.gz -2 $2_R2_nonDrosophila.fq -b SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed -f SILVA_128_SSURef_Nr99_tax_silva_trunc.ge1200bp.le2000bp.0.97.fixed.fasta -l 101 -i 294 -s 91 --phred33 -a 30
#bwa index EA_haploid_megahit_PE/EA_haploid_unmapped_PE.contigs.fa
#for name in EA87H EA71H EA119H EA49H
#do
# sh bwa.sh EA_haploid $name
#done
#bwa index EG_inbred_megahit_PE/EG_inbred_unmapped_PE.contigs.fa
#for name in EG44N EG36N
#do
# sh bwa.sh EG_inbred $name
#done
#bwa index FR_haploid_megahit_PE/FR_haploid_unmapped_PE.contigs.fa
for name in FR207H FR70H FR180H FR229H FR151H FR14H FR361H FR310H FR217H
do
sh bwa.sh FR_haploid $name
done
bwa index FR_inbred_megahit_PE/FR_inbred_unmapped_PE.contigs.fa
for name in FR109N FR312N FR112N FR219N FR110N FR59N FR157N FR11N FR126N FR198N
do
sh bwa.sh FR_inbred $name
done
bwa index KF_inbred_megahit_PE/KF_inbred_unmapped_PE.contigs.fa
for name in KF10 KF2 KF23 KF6 KF11 KF3 KF9 KF20 KF22 KF1 KF21 KF8 KF18 KF5 KF4 KF7 KF24
do
sh bwa.sh KF_inbred $name
done
bwa index SP_haploid_megahit_PE/SP_haploid_unmapped_PE.contigs.fa
for name in SP241H SP221H SP80H SP235H SP173H SP188H SP254H
do
sh bwa.sh SP_haploid $name
done
bwa index SP_inbred_megahit_PE/SP_inbred_unmapped_PE.contigs.fa
for name in SP291N SP69N SP1N SP175N SP335N SP213N SP267N SP133N SP15N SP315N SP347N SP191N SP83N
do
sh bwa.sh SP_inbred $name
done
bwa index ZI_haploid_megahit_PE/ZI_haploid_unmapped_PE.contigs.fa
for name in ZI197H ZI320H ZI353H ZI381H ZI352H ZI227H ZI114H ZI333H ZI284H ZI505H ZI344H ZI185H ZI514H
do
sh bwa.sh ZI_haploid $name
done
bwa index ZI_inbred_megahit_PE/ZI_inbred_unmapped_PE.contigs.fa
for name in ZI274N ZI31N ZI418N ZI256N ZI403N ZI366N ZI197N
do
sh bwa.sh ZI_inbred $name
done