#! /bin/bash

cd $(dirname $0)


for echantillon in 003GIDAB6c_S22_R1_001.fastq.gz 005GIDAB9c_S23_R1_001.fastq.gz 019GIDLBAPAVMc_S24_R1_001.fastq.gz 025ESTAB3c_S13_R1_001.fastq.gz 026ESTAB6c_S14_R1_001.fastq.gz 027ESTLBA9c_S15_R1_001.fastq.gz 028MAIAB3c_S16_R1_001.fastq.gz 029MAIAB9c_S17_R1_001.fastq.gz 030MAIAB15c_S18_R1_001.fastq.gz 031LAMAB3c_S6_R1_001.fastq.gz 032LAMAB9c_S7_R1_001.fastq.gz 033GHOAB3c_S8_R1_001.fastq.gz 034GHOAB9c_S9_R1_001.fastq.gz 036BOIAB3c_S1_R1_001.fastq.gz 037BOIAB9c_S2_R1_001.fastq.gz 038BOILBA11c_S3_R1_001.fastq.gz 039COUAB3c_S4_R1_001.fastq.gz 040COUAB9c_S5_R1_001.fastq.gz 041LASAB3c_S10_R1_001.fastq.gz 042LASAB9c_S11_R1_001.fastq.gz 043HOFAB4c_S19_R1_001.fastq.gz 046HOFAB9c_S20_R1_001.fastq.gz 047HOFAB12c_S21_R1_001.fastq.gz 048T3c_S12_R1_001.fastq.gz



do
 
echo java -da -Xmx400m -cp C:\/Users\/Julien\/Desktop\/bbmap\/current jgi.BBMerge in1=C:\/Users\/Julien\/Desktop\/reads\/P18007_smd_nextseq\/fastq\/"$echantillon" in2=C:\/Users\/Julien\/Desktop\/reads\/P18007_smd_nextseq\/fastq\/$(echo $echantillon |sed 's/R1/R2/') out=C:\/Users\/Julien\/Desktop\/bbmerge\/merged\/out\/$(echo $echantillon |cut -c1-11)_rna_merged.fastq outu=C:\/Users\/Julien\/Desktop\/bbmerge\/merged\/outu\/$(echo $echantillon |cut -c1-11)_rna_unmerged.fastq

echo 

done
 
