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 05-03-2010, 05:44 AM #1 upper Member   Location: Beijing ,china Join Date: May 2010 Posts: 10 Sanger FASTQ Quality Scores Here is a Sanger FASTQ : @SRR034462.9 VAB_0176_20090326_2_WT_deg_10pskmusc_461_18_311_F3 length=35 TGAGGGGTGGGGGGGTTTTTTTTTTTTTTTTTTTT +SRR034462.9 VAB_0176_20090326_2_WT_deg_10pskmusc_461_18_311_F3 length=35 '4<),/;//40-8<'%2+)'((37+0,4+2.4<0: first i convert SOLID2Sanger ,but when i handle the sangerfastq,I don't know how to convert the fourth line that the quility line;how to convert it to decimal system.preferably be perl script; Thanks a lot!
 05-03-2010, 11:27 AM #2 Zigster (Jeremy Leipzig)   Location: Philadelphia, PA Join Date: May 2009 Posts: 116 Code: ```echo "'4<),/;//40-8<'%2+)'((37+0,4+2.4<0:" | perl -e 'while(){chomp;@t=split("",\$_);\$qual.=((ord(\$_)-33)." ") for (@t);}print \$qual;' 6 19 27 8 11 14 26 14 14 19 15 12 23 27 6 4 17 10 8 6 7 7 18 22 10 15 11 19 10 17 13 19 27 15 25``` __________________ -- Jeremy Leipzig Bioinformatics Programmer -- My blog Twitter
05-03-2010, 07:20 PM   #3
upper
Member

Location: Beijing ,china

Join Date: May 2010
Posts: 10

Quote:
 Originally Posted by Zigster Code: ```echo "'4<),/;//40-8<'%2+)'((37+0,4+2.4<0:" | perl -e 'while(){chomp;@t=split("",\$_);\$qual.=((ord(\$_)-33)." ") for (@t);}print \$qual;' 6 19 27 8 11 14 26 14 14 19 15 12 23 27 6 4 17 10 8 6 7 7 18 22 10 15 11 19 10 17 13 19 27 15 25```
Zigster,
thank you very much!I fix it use your script!
Thanks!
upper

 Tags convert, decimal system, fastq, quility, sanger format