These are chat archives for dereneaton/ipyrad

14th
Aug 2018
BurnsMercedes
@BurnsMercedes
Aug 14 2018 13:51
@Siadjeu I sent you an e-mail response, I believe we have a script for this!
Siadjeu
@Siadjeu
Aug 14 2018 15:26
@BurnsMercedes Thanks! I received your e-mail I am looking forward to receive this script!
carol-rowe666
@carol-rowe666
Aug 14 2018 17:00
@BurnsMercedes Are you willing to share your script? I am looking to convert my ipyrad output for gbs2ploidy as well. That'd save reinventing the wheel.
Jenny Archibald
@jenarch
Aug 14 2018 18:44
@isaacovercast Thank you for the quick response! I did look previously in the s3_cluster_stats.txt, and I thought that ave_depth_stat was giving the average sequencing depth for loci from each accession. However, when setting clust_threshold to .80 and then to .95, the s3_cluster_stats.txt files for the two runs are completely identical, except for the filtered_bad_align column. Shouldn't the depth be different with different clustering values, because more or fewer reads end up clustered under a given locus?
carol-rowe666
@carol-rowe666
Aug 14 2018 19:22
@BurnsMercedes: Thanks for the contact information. Greatly appreciated.