These are chat archives for dereneaton/ipyrad
Hi again @dereneaton and @isaacovercast, a couple of questions.
1) Is there an easy way to exclude the merged reads from PEAR instead of including them downstream? Also, are the PEAR results stored somewhere?
2) Let's say I have a quality filtering scheme (sliding window with Trimmomatic) that I'm happy with. Is there an easy way to skip ipyrad's quality filtering? Not that double-filtering should be problematic, but it would help to keep things simple and comparable for my purposes.
Currently we don't have an option to exclude merged reads but it would be simple to add an option to do that. And they aren't actually merged by PEAR, but by vsearch. The accuracy is comparable.
Here is what step2 does now, depending on the setting of
filter_adapters to 0, 1, or 2.
if 0: it trims bases from the edges (
edit_cutsites), it filters reads that have too many Ns (
max_low_qual_bases), and it filters reads that are too short to cluster effectively (
if 1: Same as 0, plus it trims reads on the left and right at the first base with a Q score < 20, which can be modified by quality offset (
if 2: Same as 1 plus it trims Illumina adapter, or adapter+barcode for R2, if they are present in the reads.
Thanks for asking, I need to update the docs for all of these latest changes.