These are chat archives for dereneaton/ipyrad

8th
Jul 2018
Alex Linan
@alx552
Jul 08 2018 19:07
@qqsl and @isaacovercast I was able to use custom scripts from Matz lab to demultiplex and remove barcodes then I put the demultiplexed reads into ipyrad. https://github.com/z0on/2bRAD_denovo
Alex Linan
@alx552
Jul 08 2018 19:14

Hi @isaacovercast and @dereneaton ,
I have been running through the structure cookbooks with my data and structure appeared to run correctly (generated the expected output files for K6-13 2 reps each). However, when I try to visualize my structure results using clumpp I can an error. (I have clumpp installed)

tables = s.get_clumpp_table(tests)

No files ready for run_003_dios-K-3 in /home/alx552/projects/diospyros/analyses/structure/structure_ipyrad/run003_dios

the files are in the correct directory and the output files work when uploaded to clumpak, however I would like to get clumpp working with the ipyrad notebook so I can use the sort feature. A temp param file for clumpp is generated

DATATYPE 0 #
INDFILE 0 #
POPFILE 0 #
OUTFILE 0 #
MISCFILE 0 #
K 13 #
C 419 #
R 2 #
M 3 #
W 1 #
S 2 #
GREEDY_OPTION 2 #
REPEATS 50000 #
PERMUTATIONFILE 0 #
PRINT_PERMUTED_DATA 0 #
PERMUTED_DATAFILE 0 #
PRINT_EVERY_PERM 0 #
EVERY_PERMFILE 0 #
PRINT_RANDOM_INPUTORDER 0 #
RANDOM_INPUTORDERFILE 0 #
OVERRIDE_WARNINGS 0 #
ORDER_BY_RUN 1 #

Isaac Overcast
@isaacovercast
Jul 08 2018 23:07
@carol-rowe666 Yep, that's true, we don't take into account whether or not the snps are pis during the random sampling. Just because they aren't parsimony informative doesn't mean that they aren't otherwise informative, for example if you're performing population genetic analysis, then the minor allele frequency still matters.
If you are using the structure file for STRUCTURE analysis, then these singleton snps are still informative.
carol-rowe666
@carol-rowe666
Jul 08 2018 23:13
Oh, right!! Good point. Thanks for clarifying that.