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Old 05-03-2010, 05:44 AM   #1
upper
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Location: Beijing ,china

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Question 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!
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Old 05-03-2010, 11:27 AM   #2
Zigster
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Code:
echo "'4<),/;//40-8<'%2+)'((37+0,4+2.4<0:" | 
perl -e 'while(<STDIN>){chomp;@t=split("",$_);$qual.=((ord($_)-33)." ") for (@t);}print $qual;'

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Old 05-03-2010, 07:20 PM   #3
upper
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Quote:
Originally Posted by Zigster View Post
Code:
echo "'4<),/;//40-8<'%2+)'((37+0,4+2.4<0:" | 
perl -e 'while(<STDIN>){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
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