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#286 Error in quality conversion v2.1.0.0

open
nobody
bowtie (175)
5
2013-05-13
2013-05-13
Anonymous
No

Using bowtie2, bowtie2-align, or tophat2, input of a test read resulted in an incorrect quality conversion.

A FASTQ file in either illumina + 64 scale or in phred + 33 scale results in the same output string for quality in the sam/bam files. If the input is +64 and aligned with --phred64 or if the input is +33 and aligned as default, the output is the same.

The +33 version from Illumina 1.3+ was determined by both manual annotation and conversion using python 2.7 command:
''.join([chr(ord(c)-64+33) for c in r'J\^YcZKQ\J\bcdddd_YbK[_a[Z`b[b[H^^c_b^X^c\XXaOX[Xac`IM\WHWWV\ZV\\_HVMHMV\HVMVZ`cZ__MZ`']).

Below is the quality string used in the test fastq in the +64 scale, converted to +33 scale, and the bowtie2 output regardless of which was used.

INPUT+64 scale
J\^YcZKQ\J\bcdddd_YbK[_a[Z`b[b[H^^c_b^X^c\XXaOX[Xac`IM\WHWWV\ZV\\_HVMHMV\HVMVZ`cZ__MZ`

INPUT +33 scale
+=?:D;,2=+=CDEEEE@:C,<@B<;AC<C<)??D@C?9?D=99B09<9BDA*.=8)887=;7==@)7.).7=)7.7;AD;@@.;A

BWT2 Output
A;.@@;DA;7.7)=7.).7)@==7;=788)8=.*ADB9<90B99=D?9?C@D??)<C<CA;<B@<,C:@EEEEDC=+=2,;D:?=+

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