We have sample NGS data from illumina iDEA, that have PHRED+64 quality format. When you try to trim these reads by quality, you get wrongly trimmed reads.
I think we should do following steps:
Add new parameter "Encoding format" to "Trim Reads by Quality" workflow element (GUI part)Description of this parameter: "Phred quality score encoding format"By default this parameter should have value "auto" (for autodetecting of encoding format)Others values should be (more info):Phred+33Phred+64Solexa+64 (it may be not needed)
- Add autodetection of encoding format for .fastq file (example see here)
Add trimming with Phred+64 quality values