These are chat archives for dereneaton/ipyrad

28th
Sep 2017
Nirsha23
@Nirsha23
Sep 28 2017 08:38
Hi Deren,
Nirsha23
@Nirsha23
Sep 28 2017 08:45
I am using ipyrad for my ddRAD data analysis. Your tutorials are excellent and easy to follow. For my project, I pooled samples from two different species in one sequencing run. Each sample is individually barcoded. I would like to analyze the data from different species separately. Please help me. Thank you - Nirsha
Isaac Overcast
@isaacovercast
Sep 28 2017 16:58
@Nirsha23 You can achieve this by demultiplexing your all the samples first, then creating 2 branches, one for each species. You can see the documentation on branching here: http://ipyrad.readthedocs.io/tutorial_advanced_cli.html?highlight=branching#branching-assemblies
Isaac Overcast
@isaacovercast
Sep 28 2017 17:07
@rfolkert ipyrad doesn't take into account base quality when matching barcodes during demultiplexing. Are you worried about reads being misassigned? In practice this is very uncommon, so i wouldn't worry too much about qc'ing prior to demux.
rfolkert
@rfolkert
Sep 28 2017 18:11
@isaacovercast thanks for your quick reply! I am just being a bit cautious, allthough my barcodes are sequenced before the restriction site, the base-quality at the restriction site looks quit bad(PE ddRAD), therefore I was a bit worried.
Isaac Overcast
@isaacovercast
Sep 28 2017 23:14
New Version: 0.7.14: Includes fix for orientation of R2 of PE reference mapped reads.