Dear friends, Hi
I want to map my de novo transcriptome assembly to reference genome using BLAT or GMAP. Then, look at the distribution of intron lengths that can infer from those alignments.
The main story is this that the Trinity software needs a --genome_guided_max_intron parameter for its genome guided and its manual has suggested that "use a maximum intron length that makes most sense given your targeted organism"
So, I need your helps about the script(s) for mapping de novo assembly to genome: must I index the genome? must I install the BLAT same as local ncbi BLAST?
Thank you in advance