Hi, everyone, I am trying Bowtie for reference based assembly. My draft genome dataset is not from a model organism, but a related species. This data contains ~20 million 88 bp illumina reads. Because it's not resequencing of reference genome, I need to use a relatively loose parameters. Actually I only focus on genes without caring about intergenic regions. A CDS dataset of model organism can be used as a reference in this assembly. What Bowtie parameters you suggest to use? Thank you very much.
Bowtie is an aligner, not an assembler. Why don't you just use a splice-aware aligner, like tophat, or just try de novo assembly (e.g., with trinity)?
Can you actually use trinity for genome assembly? I thought it's specifically for transcript assembly.
Since biolab mentioned aligning to CDS, I'm assuming that he/she is actually doing RNAseq (though, upon rereading, this may well be incorrect!). Otherwise, yes, I think you're correct.