These are chat archives for dereneaton/ipyrad

4th
Mar 2016
Deren Eaton
@dereneaton
Mar 04 2016 05:06
In the example data set sim_rad_test when using reference method with sim_mt_genome.fa a bunch of reads get filtered out in step3 due to high indels. Any idea what's going on there? Is it passing more than one cluster to muscle alignment?
e.g.,
>A_0_2197_r1;size=18;*
TGCAGTCTGCGCCCGGGATGGATAACTTCCCTCAGTGCCGTAGACCAATAAAATGTTCACCGTCTGTGCGACAAATGATCGCCAGGCTCACAGC
>A_0_4543_r1;size=12;+
TGCAGTCCTACCATGAATGGAGTTTCTTCCTAGTTCAACATCCCCGTAATGTAATTGTAGGTGTCGAGCTTCACATGCGACCAGTAAGGAACAT
>A_0_4535_r1;size=6;+
TGCAGTCCTACTATGAATGGAGTTTCTTCCTAGTTCAACATCCCCGTAATGTAATTGTAGGTGTCGAGCTTCACATGCGACCAGTAAGGAACAT
>A_0_2208_r1;size=1;+
TGCAGTCTGCGCCCGGGATGGATAACTTCCCTCAGTGCCGTAGACCAATAAAATGTTCACCGTCTGTGCGACAAACGATCGCCAGGCTCACAGC
>A_0_4547_r1;size=1;+
TGCAGTCCTACCATGAATGGAGTTTCTTCCCAGTTCAACATCCCCGTAATGTAATTGTAGGTGTCGAGCTTCACATGCGACCAGTAAGGAACAT
^^ is a cluster from [sample].clust.gz the unaligned clusters.
Not sure if this is a new bug in reference seq. It would be super sweet to get this polished tomorrow, though, so I can use sim_rad_test as the reference example in the workshop on Sunday.
Deren Eaton
@dereneaton
Mar 04 2016 11:30
I'll be traveling most of today so I won't be online much.
Isaac Overcast
@isaacovercast
Mar 04 2016 14:18
I'll fix it.
Isaac Overcast
@isaacovercast
Mar 04 2016 15:12
This is in sim_rad_test? Which individual?
Isaac Overcast
@isaacovercast
Mar 04 2016 15:27
nvm i see it.
Isaac Overcast
@isaacovercast
Mar 04 2016 15:39
whoa, yeah something is fucked up. working on it....
Deren Eaton
@dereneaton
Mar 04 2016 19:16
Great. Thanks.