#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 


echo 'R1 .. proceed with cutadapt'
cutadapt -g CATTGATGGTGCCTACAG -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -n 2 -O 18 -m 23 -e 0.11 --match-read-wildcards --discard-untrimmed -o 1A_S50_R1_filt_ca.fastq ../secondpass/1A_S50_R1.fastq
echo 'R2 .. proceed with cutadapt'
cutadapt -a CTGTAGGCACCATCAATG -a AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -n 2 -m 28 -M 70 -e 0.11 --match-read-wildcards -o 1A_S50_R2_filt_ca.fastq ../secondpass/1A_S50_R2_filt.fastq
# first step of splicing events: isolate reads with 3'ends at 5'SS
cutadapt -a CTGTAGGCACCATCAATG -n 2 -O 8 -M 70 -e 0.11 --discard-untrimmed  --match-read-wildcards -o 1A_S50_R2_filt_ca_1stStep.fastq 1A_S50_R2_filt.fastq