These are chat archives for dereneaton/ipyrad

17th
Mar 2016
Deren Eaton
@dereneaton
Mar 17 2016 14:13
Ugh, how does this keep happening, reads are not revcomp matched correctly in the .clust file of pairgbs data now. Example below, forward starts with TGCAG, reverse ends with CTGCA but should be revcomped:
>LHW10074_128026_c1;size=1;*
TGCAGAAACTGGAAATTCTGGGGTGAATATGCAGCAGCTGGGAACTCTGGGGTnnnnAATCTGAAAACTCTGGGGGTCAAAACGCAGAATCTGGAAATTTTGGGATCAAT
>LHW10074_231561_c1;size=1;-
AAACTGGAAATTCTGGGGTGAATATGCAGCAGCTGGGAACTCTGGGGTAATnnnnAAATTCTGGGGGTCAAAACGCAGAATCTGGAATATTTGGGGTCAATCTGCA
>LHW10074_325797_c1;size=1;-
AAACTGGAAATTCTGGGGTGAATATGCAGCAGCTGGGAACTCTGGGGNAATnnnnAATCTGAGGGGGTCAAAACGCAGAATCTGGAAATTTTGGAGTCAATCTGCA
>LHW10074_359911_c1;size=1;+
TGCAGAAACTGGAAATTCTGGGGTGAATATGCAGCAGCTGGGAACTCTGGGGTnnnnTTGCTGAAAACTCTAGGGCCAAACTGAAGAATCTGAAAACTCTAGGGTCTAAT
>LHW10074_446630_c1;size=1;-
AAACTGGAAATTCTGGGGTGAATATGCAGCAGCTGGGAACTCTGGGGTAATTnnnnAAATTCTGGGGTTCAAAACGCAGAATCTGGAAATTCTGGGGTCAATTCTGCA
>LHW10074_543173_c1;size=1;+
TGCAGCAGTTGGAAATCCTGGGGTTAATATGCAGTAGCTGAGAACTCTGGGGTnnnnAATCTGAAAACTCTGGGGGTCAAAACGCAGAATCTGGAAATTTTGGGATCAAT
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at least I think that's whats going on.... I'll investigate
Deren Eaton
@dereneaton
Mar 17 2016 16:11
never mind, it looks good once it's aligned. I was being dumb.