Hello, Yes, the reference genome fasta sequence represents the forward (+) strand.
For "all fasta sequences" this is not true. Those that represent annotation (such as transcripts, example: RefSeq) can be from either strand. This type of fasta sequence represents a transcript in the direction of transcription (5'->3'). In most cases, the primary table of the source track related to the transcript fasta sequence has the reference genome alignment coordinates (including strand). Hopefully this helps, Thanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 5/31/10 2:19 PM, [email protected] wrote: > > Hi, > I have downloaded the masked genome as a ref genome to align our reads.I am > just > wondering the sequences in the fasta masked.fa files, which strand is that? > Are > all the fasta sequences are in the forward strand? please let me know. > > thanks > -dafil > > _______________________________________________ > Genome-mirror mailing list > [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome-mirror _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
