Andrew Severin

Andrew Severin

His PhD was in Biophysics/NMR spectroscopy. He did a Bioinformatics Postdoc in Soybean genetics and now runs the Genome Informatics Facility at Iowa State University. He is passionate about evolution and the science behind the genome. There is so much we don't know about how the elements in a genome interact to create the fine balance of gene expression, modification and 3D structure that create the dynamic range of phenotypes we observe. As sequencing technology continues to improve and the cost continues to decrease, we will be able to ask more complex questions that increase our understanding via comparative and translational genomics.

Learning Objective

Upon completion of this section on fastq quality scores the learner will understand the following:

  • ASSCI character encodings are used to represent quality scores
  • These numbers are converted to values between -5 and 41 to represent quality score depending on the encoding method

This table was taken from wikipedia where more information can be found on this topic.

To determine if the score is Phred+33, Phred+64 or Solexa+64, use this one-liner (you can use zcat if the fastq file is gzipped):

1
2
3
4
5
6
7
8
9
10
11
12
13
14

head -n 10000 input.fastq |\
  awk '{if(NR%4==0) printf("%s",$0);}' |  od -A n -t u1 | \
  awk 'BEGIN{min=100;max=0;} \
      {for(i=1;i<=NF;i++) \
          {if($i>max) max=$i; \
               if($i<min) min=$i;}}END \
          {if(max<=74 && min<59) \
                     print "Phred+33"; \
           else \
           if(max>73 && min>=64) \
                     print "Phred+64"; \
           else \
           if(min>=59 && min<64 && max>73) \
                     print "Solexa+64"; else print "Unknown score encoding!";}' --- [Table of contents](/introduction/terminology_index.html)