I'm trying to demultiplex some older 454 sequences (fasta + qual) so that I have individual fastq files for each barcode. I'm not looking to do a lot of quality filtering. I combined my fasta and qual files into a fastq file and then used the barcode splitter. However, the number of bases don't match the number of quality scores. When I try and filter the fastq file to remove low quality scores and limit the length of the sequences, I get the following error:
AssertionError: Invalid FASTQ file: quality score length (361) does not match sequence length (360)
I then thought maybe I need to trim the adaptors (though I really just wanted to demultiplex the data), I get the following error:
fastx_clipper: Error: invalid quality score data on line 4 (quality_tok = "FFFFFFFFFFFHHHHIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIFFFFFFF~FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEEEFFFFFF~FFFFFFFFFFFFFDDD;;;;;FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFCCCC<~DDDD???DD:::555555/==::<?DDF=???FFFFFFFFC???DDAAAAAB999946~;44/24<>>>>>>??955223??D66::DDGCCAAA??>><<001419<???=???=?~"
Any suggestions of what I'm doing wrong? This is an older data file, so I suppose its also possible that it didn't transfer from the hard drive properly.