"If fastq_quality_filter complains about invalid quality scores, try removing the -Q33 in the command; Illumina has blessed us with multiple quality score encodings."
Actually this is not accurate. My error is just "Segmentation fault (core dumped)" for not removing "-Q33".
"If you use Illumina 1.5+ without parameter -Q33 you get an error message "fastq_quality_filter: Invalid quality score value..." that clearly indicates pitfall.
But in the opposite case, when you wrongly use -Q33 for reads with Illumina quality format, error messages like
Segmentation fault (core dumped)
or
fastq_quality_filter: bug: got empty array at fastq_quality_filter.c:97
do not give a clue what is going wrong.
"
https://khmer-protocols.readthedocs.org/en/latest/metagenomics/1-quality.html
In RNASeq doc, it is mentioned. https://khmer-protocols.readthedocs.org/en/latest/mrnaseq/1-quality.html
"If fastq_quality_filter complains about invalid quality scores, try removing the -Q33 in the command; Illumina has blessed us with multiple quality score encodings."
Actually this is not accurate. My error is just "Segmentation fault (core dumped)" for not removing "-Q33".
see http://seqanswers.com/forums/showthread.php?t=9357
"If you use Illumina 1.5+ without parameter -Q33 you get an error message "fastq_quality_filter: Invalid quality score value..." that clearly indicates pitfall. But in the opposite case, when you wrongly use -Q33 for reads with Illumina quality format, error messages like Segmentation fault (core dumped) or fastq_quality_filter: bug: got empty array at fastq_quality_filter.c:97 do not give a clue what is going wrong. "