Re: FASTQ in biojava
Michael Heuer <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
On Tue, 11 May 2010, Wang, Han wrote: > I am new to biojava. I faced some problems on the numrica values of the > fastq file. I read the biojava API and found how to read in the fastq > file and get the quality from each fastq reads. Unfortunately, it just > reads the sequence of the original quality sequence rather numeric > quality values. Can someone give me some help on this problem? I will > really appreciate. On Wed, 12 May 2010, Iddo Friedberg wrote: > We're trying to get the numeric values from the biojava fastq reader. As we > understand the API, getQuality only supplies the ASCII value of the quality > string. How do we get the actual Q numeric values? That is correct, the current fastq package just handles IO to/from the Fastq memento class and conversion between different variants of the FASTQ format. The next step would be to go from a Fastq record to a Sequence with quality scores. I haven't written that part yet, guess I should get on it. :) michael _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l