These are chat archives for dereneaton/ipyrad
AGCGTGCGAGAGTnnnnAGTGCGCGAGCCGA. The first two numbers of the trim_loci param will trim the first part of the fragment and the second two numbers will trim the second part. In both cases the number specify trimming distance in bp from the 5' end of their particular part of the fragment (negative numbers count from the 3' end). For merged PE reads it will only use the first 2 numbers, since there is only one fragment to trim. Does that help?