On 31.05.2013 13:11, Susan Miller wrote: > Does Ray work with fasta input files? More specifically, would it work > with a "fastq" file that was really in fasta format (missing the quality > value lines?) I'm asking because I'm running khmer digital > normalization http://khmer.readthedocs.org/en/latest/introduction.html > on an Illumina HiSeq2000 data set, and the strip-and-split-for-assembly > script in the khmer package strips out quality info when it is > separating paired reads from singles.
Ray will work fine with FASTA files, as long as they are correctly formatted. Depending on how Ray loads the files, you may need to rename as .fa or .fasta. Note that FASTA and FASTQ format differ in the sequence name identifier character. A FASTQ file that is missing quality data does not conform to either the FASTA or the FASTQ format, because FASTQ requires both '@' and '+' tags (together with sequence and quality), and FASTA requires a '>' tag together with the sequence: >FASTA_sequence GATTACAATTAC @FASTQ_sequence GATTACAATTAC +FASTQ_sequence DEADBEEF!!!! - David ------------------------------------------------------------------------------ Get 100% visibility into Java/.NET code with AppDynamics Lite It's a free troubleshooting tool designed for production Get down to code-level detail for bottlenecks, with <2% overhead. Download for free and get started troubleshooting in minutes. http://p.sf.net/sfu/appdyn_d2d_ap2 _______________________________________________ Denovoassembler-users mailing list Denovoassembler-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/denovoassembler-users
