Hi All,

I am new to this forum and looking for advice on what the proper way is to calculate a consensus quality scores for paired end reads. Here's a concrete example of a portion of 2 aligned reads and their scores:

fragment1 - GGAGGATGCGAGCGTTATCCGG-ATTTATTGGGTTTAAA

fragment2 - CGAGGGTGCAGGGGTTAACCGGAATTTA-TGGGTGTGAA

contig - GGAGGGTGCAAGCGTTATCCGGATTTATTGGGTTTAAA

base1 base2 score1 score2

G C 33 12

G G 32 26

A A 32 12

G G 31 12

G G 33 14

A G 17 24

T T 34 12

G G 37 12

C C 37 12

G A 17 26

A G 36 24

G G 37 12

C G 38 14

G G 38 14

T T 38 24

T T 38 26

A A 38 12

T A 38 12

C C 38 12

C C 39 14

G G 38 14

G G 38 26

- A 33 14

A A 38 14

T T 38 24

T T 38 14

T T 38 14

A A 39 14

T - 39 12

T T 38 26

G G 39 12

G G 37 26

G G 39 26

T T 36 14

T G 36 26

T T 36 26

A G 37 12

A A 39 37

A A 39 31

How would you calculate the contigs quality scores? Would you suggest different methods for bases that match? bases that don't? and gap to base situations? Thanks in advance for your help!

Kindly,

Sarah

I am new to this forum and looking for advice on what the proper way is to calculate a consensus quality scores for paired end reads. Here's a concrete example of a portion of 2 aligned reads and their scores:

fragment1 - GGAGGATGCGAGCGTTATCCGG-ATTTATTGGGTTTAAA

fragment2 - CGAGGGTGCAGGGGTTAACCGGAATTTA-TGGGTGTGAA

contig - GGAGGGTGCAAGCGTTATCCGGATTTATTGGGTTTAAA

base1 base2 score1 score2

G C 33 12

G G 32 26

A A 32 12

G G 31 12

G G 33 14

A G 17 24

T T 34 12

G G 37 12

C C 37 12

G A 17 26

A G 36 24

G G 37 12

C G 38 14

G G 38 14

T T 38 24

T T 38 26

A A 38 12

T A 38 12

C C 38 12

C C 39 14

G G 38 14

G G 38 26

- A 33 14

A A 38 14

T T 38 24

T T 38 14

T T 38 14

A A 39 14

T - 39 12

T T 38 26

G G 39 12

G G 37 26

G G 39 26

T T 36 14

T G 36 26

T T 36 26

A G 37 12

A A 39 37

A A 39 31

How would you calculate the contigs quality scores? Would you suggest different methods for bases that match? bases that don't? and gap to base situations? Thanks in advance for your help!

Kindly,

Sarah

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