We have the fasta files (obviously) for the hg19 genome, we used them to create a big Bowtie index.
I was hoping not to have to keep the fasta file. Instead just look up sequences in the Bowtie index when I get chromosome locations.
I know when the alignment comes back it tells me where the alignment occurs and which fasta record (header) that it came from. So all the info is there, but I can't figure out how to pull out a sequence given a location.
Does anyone know if this is possible, or know much about the index format (perhaps I could write a little program to fish out a sequence)?
Thanks
I was hoping not to have to keep the fasta file. Instead just look up sequences in the Bowtie index when I get chromosome locations.
I know when the alignment comes back it tells me where the alignment occurs and which fasta record (header) that it came from. So all the info is there, but I can't figure out how to pull out a sequence given a location.
Does anyone know if this is possible, or know much about the index format (perhaps I could write a little program to fish out a sequence)?
Thanks
Comment