SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
What does PHRED stand for? axa9070 Illumina/Solexa 7 02-14-2017 07:33 AM
Phred value. Guigra Bioinformatics 0 05-21-2013 04:48 AM
PHRED quality score EvaRei Bioinformatics 1 10-01-2012 11:01 AM
Phred score of i jmugford Bioinformatics 1 08-12-2011 05:18 PM
another solexa/phred question crinfante Bioinformatics 8 01-22-2010 04:30 AM

Reply
 
Thread Tools
Old 04-21-2018, 09:45 AM   #1
yueli
Member
 
Location: china

Join Date: May 2013
Posts: 53
Default phred 33 or 64

Hello,

I am trying to use Trimmomatic to trim adaptor, and really confusing about my file is phred +33 or phred +64?


@J00160:122:HT2VJBBXX:8:1101:23348:1261 1:N:0:ATTACTCG+AGGCNATA
GNCTTAAATCGTGTTCCAAACCAAAATGATACAATCATGTCTCTGTTCAGCTGGGCCCANACATAAAGTACTGACNTGNTCAGNGGNANCNTCAGCAACTG
+
A#AFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJFJJJFJJFJJJJJJ#JJJJJJFJJJJJJJJ#AA#7AJJ#FF#J#F#JJJAJJJJJJ
@J00160:122:HT2VJBBXX:8:1101:23449:1261 1:N:0:ATTACTCG+AGGCNATA
GNCTGTTTCAGGCAGGGCTTACACTCTTCCCAGAGGGCCATCATGGTCTCATTGCACACNCCTGGGAGCTCCTTCNGCNTTGTNTCNGNTNCCCTGGTCTC
+
A#AFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJFJJJJJJJJJJJJJJJJJJJJJJJJJ#JJJJJJJJJJJJJJJ#AJ#FJJJ#JJ#J#J#JJJJJJJJJJ
@J00160:122:HT2VJBBXX:8:1101:23896:1261 1:N:0:ATTACTCG+AGGCTATA
CCAATCTTCTCCACACAGCCCTCCTTATGGATCGCCTTCTCGTTGAAATTAATCCCACANCCCACAGTAACATTAATGNAGCANGANTNGNGGACTCGGTT
+
AAFFFJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ#JJJJJJJJJJJJJJJJJJ#JJJJ#JJ#J#J#JJJJFJJJFF




Thanks in advance for great help!


Yue Li
yueli is offline   Reply With Quote
Old 04-21-2018, 01:15 PM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,721
Default

All new data should be phred+33. If you have data that is 5+ yr old then you have to worry about it being phred+33.
GenoMax is offline   Reply With Quote
Old 04-24-2018, 04:27 AM   #3
yueli
Member
 
Location: china

Join Date: May 2013
Posts: 53
Default

Thank you so much GenoMax!
yueli is offline   Reply With Quote
Old 04-24-2018, 05:04 AM   #4
r.rosati
Member
 
Location: Brazil

Join Date: Aug 2015
Posts: 61
Default

It is actually easy to spot (see the table here): in Phred + 33, capital letters are at the top end of the quality range (Phred score plus 33 gives an ASCII code for a capital letter when Phred is 32 to 42), while a capital letter would be an abysmal score in Phred +64. And in your case, you have "#" which is only valid for Phred +33 (ASCII code 35).
r.rosati is offline   Reply With Quote
Old 04-25-2018, 06:25 AM   #5
yueli
Member
 
Location: china

Join Date: May 2013
Posts: 53
Default

r.rosati,

Thanks for helping!
yueli is offline   Reply With Quote
Reply

Tags
phred 33 64 fastq

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 04:07 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO