#!/usr/bin/perl -w 



#out1=1A_S50_R1.fastq  out2=1A_S50_R2.fastq 
#out1=1B_S51_R1.fastq  out2=1B_S51_R2.fastq 
#out1=1C_S52_R1.fastq  out2=1C_S52_R2.fastq 
#out1=1D_S53_R1.fastq  out2=1D_S53_R2.fastq 

@files = qw(1A_S50
1B_S51
1C_S52
1D_S53
);

for($i=0;$i<4;$i++){
$name = $files[$i];

# first step of splicing events: isolate reads with 3'ends at 5'SS
system("cutadapt -a CTGTAGGCACCATCAATG -n 2 -O 8 -M 70 -e 0.11 --discard-untrimmed  --match-read-wildcards -o $name\_R2_filt_ca_1stStep.fastq ../secondpass/$name\_R2.fastq ");

}