├── R-scripts ├── SNPrelate_sample.R ├── admixture_sample.R └── normalize_gene_expression_sample.R ├── README.md ├── assembly-scripts ├── BTB_get_taxid_from_gi.py ├── ChoosePopLDinfile.py ├── NONAtsv2txt.sh ├── Q10.sh ├── Q30.sh ├── Q30AC1.sh ├── README.md ├── Rbatch.sh ├── abyss-fac.pl ├── angsd_idx_to_fst.sh ├── aseQ10.sh ├── balancetest.sh ├── bamToFastq.sh ├── bam_counts.sh ├── batch-blast-nr.sh ├── batch-blast-uniprot.sh ├── batch-bowtie2-bam-single.sh ├── batch-bowtie2-fq-flash.sh ├── batch-bowtie2-fq-paired-local.sh ├── batch-bowtie2-fq-paired-nodedup.sh ├── batch-bowtie2-fq-paired-strict.sh ├── batch-bowtie2-fq-paired-unfiltered.sh ├── batch-bowtie2-fq-paired-vsallqual.sh ├── batch-bowtie2-fq-paired.sh ├── batch-bowtie2-fq-single-dedup.sh ├── batch-bowtie2-fq-single-vsl.sh ├── batch-bowtie2-fq-single.sh ├── batch-deduplicateSE.sh ├── batch-fastqc.sh ├── batch-fastx-qualstats.sh ├── batch-filter-assembly.sh ├── batch-flash.sh ├── batch-hisat2-fq-paired.sh ├── batch-hisat2-fq-single.sh ├── batch-parse-nr.sh ├── batch-parse-uniprot.sh ├── batch-rgs.sh ├── batch-sort-index.sh ├── batch-subset-bam.sh ├── batch-template.sh ├── batch-trimmomatic-nextera.sh ├── batch-trimmomatic-pe.sh ├── batch-trimmomatic-se.sh ├── batch-wasp.sh ├── bed2gffCDS.sh ├── bed_bams_coverage.sh ├── bedfile_linkage.sh ├── bedfile_linkage_dummy.sh ├── bedfile_linkage_maxd.sh ├── blast2gffCDS.sh ├── blastx-nr.sh ├── blastx-uniprot.sh ├── blat.sh ├── cap3.sh ├── combine_cds.py ├── dummy_chrom.py ├── example-CAP3-mkm.sh ├── example_FLASH_mkm.sh ├── example_Trimmomatic_MKM.sbatch ├── example_Trinity_mkm.sbatch ├── example_fastqc_MKM.sh ├── example_tBLASTx_localdb_customout_mkm.sbatch ├── expr-divergence.R ├── extract_exons.py ├── extract_splice_sites.py ├── fastVCFcombine.sh ├── fasta2bed.sh ├── fastxQC.sh ├── filter-assembly.py ├── filterEff.sh ├── filter_fasta_by_length.sh ├── fix-weird-freebayes-snps.py ├── fix_freebayes_snps.py ├── freebayes-cluster.sh ├── freebayes-filter-hets.sh ├── freebayes-filter.sh ├── freebayes-sequential-intervals.sbatch ├── freebayes-sequential.sbatch ├── freebayes_nodes.sh ├── gdriveupload.sh ├── generate-WASP-snps.sh ├── genolike.arg ├── get-bam-counts.sh ├── get-bam-snps.sh ├── get-bed-from-list.sh ├── get-bed-from-vcf.sh ├── getGLF.sh ├── grep-good-contigs.sh ├── hets-bin.sh ├── hets.sh ├── hisat2_build_genotype_genome.py ├── hisat2_extract_HLA_vars.py ├── hisat2_extract_exons.py ├── hisat2_extract_snps_haplotypes_UCSC.py ├── hisat2_extract_snps_haplotypes_VCF.py ├── hisat2_extract_splice_sites.py ├── hisat2_genotype.py ├── hisat2_simulate_reads.py ├── hisat2_test_BRCA_genotyping.py ├── hisat2_test_HLA_genotyping.py ├── histogram.pl ├── kraken-test.sh ├── longest-isoform.pl ├── maskfasta.sh ├── merged_counts.txt ├── nathresh_af5.sh ├── ngsAdmix.sh ├── nona_af5.sh ├── parallel.sh ├── parallel_sbatch.sh ├── parse-blast-ncbi-xml.py ├── parse-uniprot-xml.py ├── prepDE.py ├── prim.sh ├── run-freebayes-cluster.sh ├── samtools_merge.sh ├── subset-bams-for-wasp.sh ├── touch-contigs.sh ├── tsv-ase-bin.R ├── tsv-ase.R ├── vcf-filter-05.sh ├── vcf-filter-all-no-doubletons.sh ├── vcf-filter-all-no-singletons.sh ├── vcf-filter-all.sh ├── vcf-filter-nomissing-maf05-allgq30.sh ├── vcf-filter-nomissing-maf05-eSNPs.sh ├── vcf-filter-nomissing-maf05-qual30.sh ├── vcf-filter-qual30.sh ├── vcf-filter-tsv.sh ├── vcfcombine.sh ├── vcftools-012genotype-matrix.sh ├── vcftools-snpfilter.sh └── wasp-bam.sh ├── guide-to-R-scripts.md └── guide-to-assembly-scripts.md /R-scripts/SNPrelate_sample.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hopkinsmarinestation/Population-Genomics-via-RNAseq/HEAD/R-scripts/SNPrelate_sample.R -------------------------------------------------------------------------------- /R-scripts/admixture_sample.R: -------------------------------------------------------------------------------- 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