These are chat archives for dereneaton/ipyrad

11th
May 2016
Cycadales
@Cycadales
May 11 2016 06:58

Sorry Guys I have another question as there seems that there might be an issue with step 2 (or my data) as I am losing a significant amount of data. I am using PE ezRAD but using two enzymes to cut sequence data and I have tried a few different setting in the params file for datatypes. Firstly I tried pairedGBS and secondly I tried pairddrad with no difference. This is my results which were consistent are there any setting I can use to correct it?; Summary stats of Assembly cycas

                   state  reads_raw  reads_filtered
Ccal-15-18-10_S24_001 2 3107633 180323
Ccal-15-18-2_S25_001 2 3138147 224111
Ccal-15-18-3_S26_001 2 3092806 225864
Ccal-15-18-4_S27_001 2 3278386 257578
Ccal-15-18-5_S28_001 2 3103345 228464
Ccal-15-18-6_S29_001 2 6432044 422360
Ccal-15-18-7_S30_001 2 3129772 205775
Ccal-15-18-9_S32_001 2 4244585 294857