On 30/05/13 09:39 PM, David Eccles (gringer) wrote: > 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. >
Jean-François Erdelyi added some code so that Ray will read both .fa and .fasta files for fasta files. For fastq files, accepted extensions are .fq and .fastq I think. > 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!!!! > Thanks David for this thorough answer. > - 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 > ------------------------------------------------------------------------------ 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
