You can now run smartpca on that parameter file and submit to SLURM via: The last line contains a flag that is recommended for low coverage and ancient data. The next line contains a file with the list of populations that you want to use to construct the PCA, as discussed above. The next two lines are two output files, and you have to make sure the directory where these two files will be written into exists. The first three lines contain the three genotype files you generated from merging your test samples with the HO data set, so the output of the mergeit program. txt poplistname : / home / adminschif / GAworkshop / pca_populations. txt evaloutname : / data / schiffels / GAworkshop / pca / MyProject. ![]() txt evecoutname : / data / schiffels / GAworkshop / pca / MyProject. ![]() txt indivname : / data / schiffels / GAworkshop / genotyping / MyProject. txt snpname : / data / schiffels / GAworkshop / genotyping / MyProject. Genotypename : / data / schiffels / GAworkshop / genotyping / MyProject.
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