These are chat archives for dereneaton/ipyrad

24th
Apr 2016
Cycadales
@Cycadales
Apr 24 2016 11:40
Hi Daren, wondering if you got that data ok? I have just tried to load some illumina NextSeq data into (just one sample 8 seperate files) ipyrad and it seemed to recognise each lane as a seperate sample. Do you know a way around this? I know the software is still in development.
Cycadales
@Cycadales
Apr 24 2016 12:02
Daren, This was demultiplexed data and this came up during step one.
Isaac Overcast
@isaacovercast
Apr 24 2016 15:30

Oh my god dude that's insannne!

Looks like we can demultiplex a full lane of data in about 15 mins now.

Deren Eaton
@dereneaton
Apr 24 2016 17:01
Hey @cycadales, You can just concatenate the multiple data files for each individual before starting ipyrad analysis. Google how to concatenate gzipped files for directions.
Be sure to concatenate R1s and R2s separately, and in the same order for each sample.
So that the paired reads line up.
Deren Eaton
@dereneaton
Apr 24 2016 17:38
@isaacovercast , SE RAD is good to go again :+1:
PE data needs some work, I'll give it a go at PE ddRAD if you can keep working on the ref assembly stuff.
The large h5 array in step6 gets too large at the moment on really large data sets. I think it needs better chunking so that it can be compressed and read in with lower memory overhead. On my todos.
Isaac Overcast
@isaacovercast
Apr 24 2016 18:29
nice. i'll check it out. :clap: :sparkles:
Cycadales
@Cycadales
Apr 24 2016 22:26
Thanks Daren. I will give that a go