I have multiple libraries supposedly made at insert sizes from 6kb to 20kb.
I have un-scaffolded contigs (~30X coverage) from a previous assembly of this genome. There isn't a scaffolded assembly available right now.
What is the best way to go about estimating insert sizes for these long insert libraries?
I've tried mapping the libraries back to contigs > 3kb with bowtie2 specifying -I -X parameters (minimum and maximum insert sizes). I've tried different minimums and the insert size distribution seem to center around this minimum insert size paramter. This makes me think that bowtie2 is just not handling mapping long insert sizes correctly.
Should I be using another mapper? There are only ~100,000 contigs > 3kb in the genome contigs which resulted in only ~10k-100k reads mapping among the libraries. Should I even bother trying to estimate insert size from these contigs? Should I re-contig assemble with the current reads?