Open andreas-wilm opened 9 years ago
Could you paste the output files that were incorrectly recognised? Maybe the first several pairs of reads are enough. Thanks!
Here's an example (after processing with SeqMerge) which is correctly detected by FastQC but not skewer:
@M01853:160:000000000-ADF3H:1:1101:15279:1355 1:N:0:6
GTCCGTCCTCCTCCTCCCCCGTCTCCGCCCCCCGGCCCCGCGTCCTCCCTCGGGAGGGCGCGCGGGTCGGGGCGGCGGCCTGGGGGCGGGGAGCGGTCGGGCGGCGGCGGTCGGCGGGCTGTAGGCACCATCAAT
+
]]]]]]]]]]]S]SS]]]]]]]S]]T]]]]]S]]]]]]]]]]]]]]]]]]]]]]Q]]]]]]]]]]]U]]]]]]]]]]]]]]]]]]]]]]]]]]]]]9]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]]
Andreas
Hi Andreas, According to http://en.wikipedia.org/wiki/FASTQ_format, the quality value could not be greater than 41. In this sense, Q60 is a non-standard scheme. However maybe we can support this scheme in the future.
SeqPrep merges overlapping paired-end fastq files. It bumps up quality scores in overlapping scores accordingly (i.e. two agreeing bases with Q30 result in a Q60 base output). Quality encoding in SeqPrep output files is incorrectly recognised by Skewer as 'Solexa/Illumina 1.3+/Illumina 1.5+' instead of correctly 'Sanger/Illumina 1.8+'
Andreas