From 2f2cb311bfa6d7a0b643a5b36af727b0be929de8 Mon Sep 17 00:00:00 2001 From: Shifu Chen Date: Thu, 10 Mar 2016 22:03:41 +0800 Subject: [PATCH] change default parameter for low quality number threshold --- after.py | 8 ++++---- preprocesser.py | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/after.py b/after.py index c92ae2c..ba72171 100755 --- a/after.py +++ b/after.py @@ -41,10 +41,10 @@ def parseCommand(): help = "number of bases to be trimmed in the tail of read. -1 means auto detect") parser.add_option("", "--trim_pair_same", dest = "trim_pair_same", default = "true", help = "use same trimming configuration for read1 and read2 to keep their sequence length identical, default is true") - parser.add_option("-q", "--qualified_quality_phred", dest = "qualified_quality_phred", default = 20, type = "int", - help = "the quality value that a base is qualifyed. Default 20 means phred base quality >=Q20 is qualified.") - parser.add_option("-u", "--unqualified_base_limit", dest = "unqualified_base_limit", default = 0, type = "int", - help = "if exists more than unqualified_base_limit bases that quality is lower than qualified quality, then this read/pair is bad. Default 0 means do not filter reads by low quality base count") + parser.add_option("-q", "--qualified_quality_phred", dest = "qualified_quality_phred", default = 14, type = "int", + help = "the quality value that a base is qualifyed. Default 14 means phred base quality >=Q14 is qualified.") + parser.add_option("-u", "--unqualified_base_limit", dest = "unqualified_base_limit", default = 10, type = "int", + help = "if exists more than unqualified_base_limit bases that quality is lower than qualified quality, then this read/pair is bad. Default is 10") parser.add_option("-p", "--poly_size_limit", dest = "poly_size_limit", default = 40, type = "int", help = "if exists one polyX(polyG means GGGGGGGGG...), and its length is >= poly_size_limit, then this read/pair is bad. Default is 40") parser.add_option("-a", "--allow_mismatch_in_poly", dest = "allow_mismatch_in_poly", default = 5, type = "int", diff --git a/preprocesser.py b/preprocesser.py index 54e9e5d..59ee4c8 100755 --- a/preprocesser.py +++ b/preprocesser.py @@ -468,7 +468,7 @@ def run(self): #write to good writeReads(r1, r2, i1, i2, good_read1_file, good_read2_file, good_index1_file, good_index2_file, None) GOOD += 1 - #if TOTAL > 100000:break + #if TOTAL > 10000:break #close all files good_read1_file.flush()