phred 33 or 64

[yueli]

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

[GenoMax]

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.

[yueli]

Thank you so much GenoMax！

[r.rosati]

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).

[yueli]

r.rosati,

Thanks for helping!