These are chat archives for dereneaton/ipyrad

25th
Apr 2017
elviscat
@elviscat
Apr 25 2017 03:02
Hi @dereneaton, a simple question: I have a bunch of fastq files from Ion Torrent AmpliSeq but it seems pyRAD cannot read it. Is anyone having the same issue with me?
Deren Eaton
@dereneaton
Apr 25 2017 03:16
Hi @elviscat are you using pyRAD or ipyrad? I have never analyzed Ion Torrent Ampliseq data before, but my understanding is that it is different from RAD-seq-type data in that you develop primers to target across genes with partially overlapping tiled reads. If that is the case then I think some other software might work better. pyRAD and ipyrad assume that your sequenced loci will share a fragmented end and therefore lineup without tiling. I may be wrong though, I don't know all the details of that method. If the data are like RAD-seq then you should be able to assemble the loci in ipyrad, but you may have to tweak some options if read lengths are much longer than Illumina short reads.
Deren Eaton
@dereneaton
Apr 25 2017 18:22
v.0.6.16 is now available. It has several new features and bug fixes including: Step 6 aligning is about 30% faster and the .alleles output is now supported. See other minor changes here: https://github.com/dereneaton/ipyrad/blob/master/docs/releasenotes.rst#0616