[BioC] report a possble bug in shortread

Wang Peter wng.peter at gmail.com
Fri Nov 30 04:48:59 CET 2012


i read the fastq file and let the function identify the quality score

		if(iteration==1)#
		{
			score_sys = data.class(quality(reads));	
		}
		if(score_sys =="SFastqQuality")#Phred+64
		{
		  do something
		}
		if(score_sys =="FastqQuality")#Phred+33
		{
		 do something
		}


but the score_sys=SFastqQuality, the data is Phred+33

see the quality line
HHHHHHHHHHHHHHHHHHGHHHHHHDDCDD#?CCBCDDDCHEHHHHHHHHHHHFH7

-- 
shan gao
Room 231(Dr.Fei lab)
Boyce Thompson Institute
Cornell University
Tower Road, Ithaca, NY 14853-1801
Office phone: 1-607-254-1267(day)
Official email:sg839 at cornell.edu
Facebook:http://www.facebook.com/profile.php?id=100001986532253



More information about the Bioconductor mailing list