Fastq quality scoring

The clc_quality_trim program requires an ASCII offset value for the quality scores in fastq formatted files. The default behavior is to automatically detect this offset from the input data, but in case that this fails it is also possible to set the offset manually. To set the offset correctly you need to know the pipeline used to generate the original data and then set the offset accordingly using the -f option. Some examples of standard offset values for Illumina pipelines are:

For example, the following command would stipulate a minimum quality value of 10 and an offset of 33. The program will return the longest region for each read that fulfills these criteria. Reads that do not have regions that make the criteria cutoffs will be discarded.

quality_trim -r smallfile.fastq -c 10  -f 33 -o smallfile_trimmed.fasta

Note that the cutoff can be a negative value for the Solexa pipeline.