TN1_other_NCBI_reads_PE_trimmomatic_withpalindrome_minlen50.py

#####################################################################
# Date: August 2, 2014                                               #
# Author: Jerome P. Panibe                                          #
#                                                                   #
# This script will remove the adapters in raw TNG67 mate-pair data  #
#                                                                   #
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import os

files150=["ERR619929", \
"ERR619928", \
"ERR619927", \
"ERR619926", \
"ERR619925", \
"ERR619924", \
"ERR619923", \
"ERR619922", \
"ERR619921", \
"ERR619920", \
"ERR619919", \
"ERR619918", \
"ERR619917", \
"ERR619916"]



i=0
while i<len(files150):
	os.chdir('/home/jpanibe/SRA_Data')
	os.system('java -jar /home/jpanibe/CLC_Data/Trimmomatic-0.39/Trimmomatic-0.39/trimmomatic-0.39.jar PE -threads 16 -trimlog %s_trimmomatic_TN1_other_NCBI_reads.txt %s_1.fastq %s_2.fastq %s_trimmomatic_minlen50_R1.fastq %s_trimmomatic_minlen50_R1.fastq_noadapter_s1_se %s_trimmomatic_minlen50_R2.fastq %s_trimmomatic_minlen50_R2.fastq_noadapter_s2_se ILLUMINACLIP:/home/jpanibe/CLC_Data/Trimmomatic-0.39/Trimmomatic-0.39/adapters/adapters.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:50 CROP:82' % (files150[i],files150[i],files150[i],files150[i],files150[i],files150[i],files150[i]))
	i+=1