These are chat archives for dereneaton/ipyrad

9th
Dec 2015
Deren Eaton
@dereneaton
Dec 09 2015 00:27
I got my hands on a chloroplast genome today for a group of plants I also have RAD data for. Once the refseq is up and ready it can be a good little test for using refmapping to separate genomic from plastid data.
Isaac Overcast
@isaacovercast
Dec 09 2015 14:31
Oh sweet, that's super useful!
Isaac Overcast
@isaacovercast
Dec 09 2015 14:36
Here's a nasty problem i had yesterday: https://github.com/dereneaton/ipyrad/wiki/samtools-pileup-hell
Isaac Overcast
@isaacovercast
Dec 09 2015 19:28
Question: My understanding is that in some cases the 2nd read of a PE pair is on the forward strand, and in some cases it's on the reverse strand. Same question as earlier w/ GBS, should i take the complement of the reverse strand so both pairs are on the forward strand in all cases for PE? I assume this is what you're already doing cuz it makes sense, but want to double check.. PS - fixed the nasty probem, from earlier, so only look at it if yr curious.