I've just been revisiting differences in quality scores between different fastq format (re-reading Cock et. al. 2010 Nucleic Acids Research - what a MESS Illumina has made of the fastq format).
In any case, perhaps I am missing something but am trying to figure out how FastX-Toolkit (I'm using version fastx_toolkit-0.0.13.tar.bz2) is both reading in, scoring, and filtering on quality scores (ie., is it using solexa_fastq, sanger_fastq, illuminav1.3+_fastq quality scores or can it handle all). When plotting out the graph of quality scores, you get a range from -15 to 45 which corresponds to a range of 60 but doesn't seem to correspond to any of these published fastq formats ?*&!. Since this is 2010 and we've been using Illumina 1.3+ for some time now and I've read here on SEQ-ANSWERS that the first two quality scores (0,1) are not included so the range for Illumina 1.3+ quality scores is really 60, I'm assuming that FastX is both reading in and filtering on Illumina pipeline v1.3+ fastq format quality scores. I'd feel better though is someone else could confirm!
Thanks!
In any case, perhaps I am missing something but am trying to figure out how FastX-Toolkit (I'm using version fastx_toolkit-0.0.13.tar.bz2) is both reading in, scoring, and filtering on quality scores (ie., is it using solexa_fastq, sanger_fastq, illuminav1.3+_fastq quality scores or can it handle all). When plotting out the graph of quality scores, you get a range from -15 to 45 which corresponds to a range of 60 but doesn't seem to correspond to any of these published fastq formats ?*&!. Since this is 2010 and we've been using Illumina 1.3+ for some time now and I've read here on SEQ-ANSWERS that the first two quality scores (0,1) are not included so the range for Illumina 1.3+ quality scores is really 60, I'm assuming that FastX is both reading in and filtering on Illumina pipeline v1.3+ fastq format quality scores. I'd feel better though is someone else could confirm!
Thanks!
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