Move RAD-Seq tutorials to ecology topic

galaxyproject · Sep 12, 2019 · bfc1c8c · bfc1c8c
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diff --git a/...D1_SNP_calling/RAD1_SNP_calling_Fasta.png → ...D1_SNP_calling/RAD1_SNP_calling_Fasta.png b/...D1_SNP_calling/RAD1_SNP_calling_Fasta.png → ...D1_SNP_calling/RAD1_SNP_calling_Fasta.png
diff --git a/...lling/RAD1_SNP_calling_female_alleles.png → ...lling/RAD1_SNP_calling_female_alleles.png b/...lling/RAD1_SNP_calling_female_alleles.png → ...lling/RAD1_SNP_calling_female_alleles.png
diff --git a/...alling/RAD1_SNP_calling_female_models.png → ...alling/RAD1_SNP_calling_female_models.png b/...alling/RAD1_SNP_calling_female_models.png → ...alling/RAD1_SNP_calling_female_models.png
diff --git a/..._calling/RAD1_SNP_calling_female_snps.png → ..._calling/RAD1_SNP_calling_female_snps.png b/..._calling/RAD1_SNP_calling_female_snps.png → ..._calling/RAD1_SNP_calling_female_snps.png
diff --git a/..._calling/RAD1_SNP_calling_female_tags.png → ..._calling/RAD1_SNP_calling_female_tags.png b/..._calling/RAD1_SNP_calling_female_tags.png → ..._calling/RAD1_SNP_calling_female_tags.png
diff --git a/...calling_female_tags_SNP_visualization.png → ...calling_female_tags_SNP_visualization.png b/...calling_female_tags_SNP_visualization.png → ...calling_female_tags_SNP_visualization.png
diff --git a/...g_female_tags_primary_secondary_reads.png → ...g_female_tags_primary_secondary_reads.png b/...g_female_tags_primary_secondary_reads.png → ...g_female_tags_primary_secondary_reads.png
diff --git a/...P_calling/RAD1_SNP_calling_ustacks_in.png → ...P_calling/RAD1_SNP_calling_ustacks_in.png b/...P_calling/RAD1_SNP_calling_ustacks_in.png → ...P_calling/RAD1_SNP_calling_ustacks_in.png
diff --git a/..._calling/RAD1_SNP_calling_ustacks_out.png → ..._calling/RAD1_SNP_calling_ustacks_out.png b/..._calling/RAD1_SNP_calling_ustacks_out.png → ..._calling/RAD1_SNP_calling_ustacks_out.png
diff --git a/...etic_Map/Genetic_map_CrossPollination.png → ...etic_Map/Genetic_map_CrossPollination.png b/...etic_Map/Genetic_map_CrossPollination.png → ...etic_Map/Genetic_map_CrossPollination.png
diff --git a/...mages/RAD2_Genetic_Map/Genetic_map_F2.png → ...mages/RAD2_Genetic_Map/Genetic_map_F2.png b/...mages/RAD2_Genetic_Map/Genetic_map_F2.png → ...mages/RAD2_Genetic_Map/Genetic_map_F2.png
diff --git a/.../images/RAD2_Genetic_Map/Genotypes_in.png → .../images/RAD2_Genetic_Map/Genotypes_in.png b/.../images/RAD2_Genetic_Map/Genotypes_in.png → .../images/RAD2_Genetic_Map/Genotypes_in.png
diff --git a/...Genetic_Map/Input_demultiplexed_files.png → ...Genetic_Map/Input_demultiplexed_files.png b/...Genetic_Map/Input_demultiplexed_files.png → ...Genetic_Map/Input_demultiplexed_files.png
diff --git a/...D2_Genetic_Map/denovo_map_log_cstacks.png → ...D2_Genetic_Map/denovo_map_log_cstacks.png b/...D2_Genetic_Map/denovo_map_log_cstacks.png → ...D2_Genetic_Map/denovo_map_log_cstacks.png
diff --git a/...s/RAD2_Genetic_Map/denovo_map_log_end.png → ...s/RAD2_Genetic_Map/denovo_map_log_end.png b/...s/RAD2_Genetic_Map/denovo_map_log_end.png → ...s/RAD2_Genetic_Map/denovo_map_log_end.png
diff --git a/...Genetic_Map/denovo_map_log_genotypes1.png → ...Genetic_Map/denovo_map_log_genotypes1.png b/...Genetic_Map/denovo_map_log_genotypes1.png → ...Genetic_Map/denovo_map_log_genotypes1.png
diff --git a/...Genetic_Map/denovo_map_log_genotypes2.png → ...Genetic_Map/denovo_map_log_genotypes2.png b/...Genetic_Map/denovo_map_log_genotypes2.png → ...Genetic_Map/denovo_map_log_genotypes2.png
diff --git a/...D2_Genetic_Map/denovo_map_log_sstacks.png → ...D2_Genetic_Map/denovo_map_log_sstacks.png b/...D2_Genetic_Map/denovo_map_log_sstacks.png → ...D2_Genetic_Map/denovo_map_log_sstacks.png
diff --git a/...s/RAD2_Genetic_Map/denovo_map_log_top.png → ...s/RAD2_Genetic_Map/denovo_map_log_top.png b/...s/RAD2_Genetic_Map/denovo_map_log_top.png → ...s/RAD2_Genetic_Map/denovo_map_log_top.png
diff --git a/...D2_Genetic_Map/denovo_map_log_ustacks.png → ...D2_Genetic_Map/denovo_map_log_ustacks.png b/...D2_Genetic_Map/denovo_map_log_ustacks.png → ...D2_Genetic_Map/denovo_map_log_ustacks.png
diff --git a/.../RAD2_Genetic_Map/denovo_map_matches1.PNG → .../RAD2_Genetic_Map/denovo_map_matches1.PNG b/.../RAD2_Genetic_Map/denovo_map_matches1.PNG → .../RAD2_Genetic_Map/denovo_map_matches1.PNG
diff --git a/.../RAD2_Genetic_Map/denovo_map_matches2.png → .../RAD2_Genetic_Map/denovo_map_matches2.png b/.../RAD2_Genetic_Map/denovo_map_matches2.png → .../RAD2_Genetic_Map/denovo_map_matches2.png
diff --git a/...denovo_map_matches_alleles_haplotypes.png → ...denovo_map_matches_alleles_haplotypes.png b/...denovo_map_matches_alleles_haplotypes.png → ...denovo_map_matches_alleles_haplotypes.png
diff --git a/...enovo_map_matches_alleles_male_female.png → ...enovo_map_matches_alleles_male_female.png b/...enovo_map_matches_alleles_male_female.png → ...enovo_map_matches_alleles_male_female.png
diff --git a/...enetic_Map/denovo_map_matches_markers.png → ...enetic_Map/denovo_map_matches_markers.png b/...enetic_Map/denovo_map_matches_markers.png → ...enetic_Map/denovo_map_matches_markers.png
diff --git a/...2_Genetic_Map/denovo_map_matches_snps.png → ...2_Genetic_Map/denovo_map_matches_snps.png b/...2_Genetic_Map/denovo_map_matches_snps.png → ...2_Genetic_Map/denovo_map_matches_snps.png
diff --git a/...p/denovo_map_matches_snps_male_female.png → ...p/denovo_map_matches_snps_male_female.png b/...p/denovo_map_matches_snps_male_female.png → ...p/denovo_map_matches_snps_male_female.png
diff --git a/.../images/RAD2_Genetic_Map/denovomap_in.png → .../images/RAD2_Genetic_Map/denovomap_in.png b/.../images/RAD2_Genetic_Map/denovomap_in.png → .../images/RAD2_Genetic_Map/denovomap_in.png
diff --git a/...images/RAD2_Genetic_Map/denovomap_out.png → ...images/RAD2_Genetic_Map/denovomap_out.png b/...images/RAD2_Genetic_Map/denovomap_out.png → ...images/RAD2_Genetic_Map/denovomap_out.png
diff --git a/...ic_Map/genotypes_automatic_correction.png → ...ic_Map/genotypes_automatic_correction.png b/...ic_Map/genotypes_automatic_correction.png → ...ic_Map/genotypes_automatic_correction.png
diff --git a/...images/RAD2_Genetic_Map/genotypes_tsv.png → ...images/RAD2_Genetic_Map/genotypes_tsv.png b/...images/RAD2_Genetic_Map/genotypes_tsv.png → ...images/RAD2_Genetic_Map/genotypes_tsv.png
diff --git a/...images/RAD2_Genetic_Map/genotypes_txt.png → ...images/RAD2_Genetic_Map/genotypes_txt.png b/...images/RAD2_Genetic_Map/genotypes_txt.png → ...images/RAD2_Genetic_Map/genotypes_txt.png
diff --git a/...mages/RAD2_Genetic_Map/haplotypes_tsv.png → ...mages/RAD2_Genetic_Map/haplotypes_tsv.png b/...mages/RAD2_Genetic_Map/haplotypes_tsv.png → ...mages/RAD2_Genetic_Map/haplotypes_tsv.png
diff --git a/...is/images/RAD3_Mini-contig/Input_data.png → ...gy/images/RAD3_Mini-contig/Input_data.png b/...is/images/RAD3_Mini-contig/Input_data.png → ...gy/images/RAD3_Mini-contig/Input_data.png
diff --git a/...es/RAD3_Mini-contig/assemblereadpairs.png → ...es/RAD3_Mini-contig/assemblereadpairs.png b/...es/RAD3_Mini-contig/assemblereadpairs.png → ...es/RAD3_Mini-contig/assemblereadpairs.png
diff --git a/...sis/images/RAD3_Mini-contig/denovomap.png → ...ogy/images/RAD3_Mini-contig/denovomap.png b/...sis/images/RAD3_Mini-contig/denovomap.png → ...ogy/images/RAD3_Mini-contig/denovomap.png
diff --git a/...ulation_Genomics/Hohenlohe_et_al_2010.png → ...ulation_Genomics/Hohenlohe_et_al_2010.png b/...ulation_Genomics/Hohenlohe_et_al_2010.png → ...ulation_Genomics/Hohenlohe_et_al_2010.png
diff --git a/...D4_Population_Genomics/Input_data_ENA.png → ...D4_Population_Genomics/Input_data_ENA.png b/...D4_Population_Genomics/Input_data_ENA.png → ...D4_Population_Genomics/Input_data_ENA.png
diff --git a/...n_Genomics/Process_radtags_charts_end.PNG → ...n_Genomics/Process_radtags_charts_end.PNG b/...n_Genomics/Process_radtags_charts_end.PNG → ...n_Genomics/Process_radtags_charts_end.PNG
diff --git a/...rocess_radtags_charts_tablemodif_view.PNG → ...rocess_radtags_charts_tablemodif_view.PNG b/...rocess_radtags_charts_tablemodif_view.PNG → ...rocess_radtags_charts_tablemodif_view.PNG
diff --git a/...opulation_Genomics/Process_radtags_in.png → ...opulation_Genomics/Process_radtags_in.png b/...opulation_Genomics/Process_radtags_in.png → ...opulation_Genomics/Process_radtags_in.png
diff --git a/...enomics/Process_radtags_out_parameter.png → ...enomics/Process_radtags_out_parameter.png b/...enomics/Process_radtags_out_parameter.png → ...enomics/Process_radtags_out_parameter.png
diff --git a/...nomics/Process_radtags_out_parameter2.png → ...nomics/Process_radtags_out_parameter2.png b/...nomics/Process_radtags_out_parameter2.png → ...nomics/Process_radtags_out_parameter2.png
diff --git a/...Population_Genomics/denovo/denovo_out.png → ...Population_Genomics/denovo/denovo_out.png b/...Population_Genomics/denovo/denovo_out.png → ...Population_Genomics/denovo/denovo_out.png
diff --git a/...enomics/denovo/output_X_fst_Y-Z_tsv_1.png → ...enomics/denovo/output_X_fst_Y-Z_tsv_1.png b/...enomics/denovo/output_X_fst_Y-Z_tsv_1.png → ...enomics/denovo/output_X_fst_Y-Z_tsv_1.png
diff --git a/...enomics/denovo/output_X_fst_Y-Z_tsv_2.png → ...enomics/denovo/output_X_fst_Y-Z_tsv_2.png b/...enomics/denovo/output_X_fst_Y-Z_tsv_2.png → ...enomics/denovo/output_X_fst_Y-Z_tsv_2.png
diff --git a/...cs/denovo/output_sumstats_summary_tsv.png → ...cs/denovo/output_sumstats_summary_tsv.png b/...cs/denovo/output_sumstats_summary_tsv.png → ...cs/denovo/output_sumstats_summary_tsv.png
diff --git a/...Genomics/denovo/output_sumstats_tsv_1.png → ...Genomics/denovo/output_sumstats_tsv_1.png b/...Genomics/denovo/output_sumstats_tsv_1.png → ...Genomics/denovo/output_sumstats_tsv_1.png
diff --git a/...Genomics/denovo/output_sumstats_tsv_2.png → ...Genomics/denovo/output_sumstats_tsv_2.png b/...Genomics/denovo/output_sumstats_tsv_2.png → ...Genomics/denovo/output_sumstats_tsv_2.png
diff --git a/...lation_Genomics/denovo/populations_in.png → ...lation_Genomics/denovo/populations_in.png b/...lation_Genomics/denovo/populations_in.png → ...lation_Genomics/denovo/populations_in.png
diff --git a/...ation_Genomics/denovo/populations_log.png → ...ation_Genomics/denovo/populations_log.png b/...ation_Genomics/denovo/populations_log.png → ...ation_Genomics/denovo/populations_log.png
diff --git a/...ation_Genomics/denovo/populations_out.png → ...ation_Genomics/denovo/populations_out.png b/...ation_Genomics/denovo/populations_out.png → ...ation_Genomics/denovo/populations_out.png
diff --git a/...ages/RAD4_Population_Genomics/multiqc.PNG → ...ages/RAD4_Population_Genomics/multiqc.PNG b/...ages/RAD4_Population_Genomics/multiqc.PNG → ...ages/RAD4_Population_Genomics/multiqc.PNG
diff --git a/...ation_Genomics/reference/Map_with_BWA.png → ...ation_Genomics/reference/Map_with_BWA.png b/...ation_Genomics/reference/Map_with_BWA.png → ...ation_Genomics/reference/Map_with_BWA.png
diff --git a/...ation_Genomics/reference/custom_build.png → ...ation_Genomics/reference/custom_build.png b/...ation_Genomics/reference/custom_build.png → ...ation_Genomics/reference/custom_build.png
diff --git a/...cs/reference/custom_build_association.png → ...cs/reference/custom_build_association.png b/...cs/reference/custom_build_association.png → ...cs/reference/custom_build_association.png
diff --git a/...nomics/reference/cut_columns_barcodes.png → ...nomics/reference/cut_columns_barcodes.png b/...nomics/reference/cut_columns_barcodes.png → ...nomics/reference/cut_columns_barcodes.png
diff --git a/...on_Genomics/reference/populations_out.png → ...on_Genomics/reference/populations_out.png b/...on_Genomics/reference/populations_out.png → ...on_Genomics/reference/populations_out.png
diff --git a/...n_Genomics/reference/reference_map_in.png → ...n_Genomics/reference/reference_map_in.png b/...n_Genomics/reference/reference_map_in.png → ...n_Genomics/reference/reference_map_in.png
diff --git a/...ics/reference/trackster_visualization.PNG → ...ics/reference/trackster_visualization.PNG b/...ics/reference/trackster_visualization.PNG → ...ics/reference/trackster_visualization.PNG
diff --git a/...analysis/images/denovo_based_workflow.PNG → .../ecology/images/denovo_based_workflow.PNG b/...analysis/images/denovo_based_workflow.PNG → .../ecology/images/denovo_based_workflow.PNG
diff --git a/...-analysis/images/genetic_map_workflow.PNG → ...s/ecology/images/genetic_map_workflow.PNG b/...-analysis/images/genetic_map_workflow.PNG → ...s/ecology/images/genetic_map_workflow.PNG
diff --git a/...ce-analysis/images/ref_based_workflow.PNG → topics/ecology/images/ref_based_workflow.PNG b/...ce-analysis/images/ref_based_workflow.PNG → topics/ecology/images/ref_based_workflow.PNG
diff --git a/...torials/de-novo-rad-seq/data-library.yaml → ...torials/de-novo-rad-seq/data-library.yaml b/...torials/de-novo-rad-seq/data-library.yaml → ...torials/de-novo-rad-seq/data-library.yaml
diff --git a/...tutorials/de-novo-rad-seq/tours/tour.yaml → ...tutorials/de-novo-rad-seq/tours/tour.yaml b/...tutorials/de-novo-rad-seq/tours/tour.yaml → ...tutorials/de-novo-rad-seq/tours/tour.yaml
diff --git a/...sis/tutorials/de-novo-rad-seq/tutorial.md → ...ogy/tutorials/de-novo-rad-seq/tutorial.md b/...sis/tutorials/de-novo-rad-seq/tutorial.md → ...ogy/tutorials/de-novo-rad-seq/tutorial.md
@@ -22,7 +22,7 @@ In the study of [Hohenlohe *et al.* 2010](http://journals.plos.org/plosgenetics/
 
 ![Abstract of the paper on Population Genomics](../../images/RAD4_Population_Genomics/Hohenlohe_et_al_2010.png)
 
-We here proposed to re-analyze these data at least until the population genomics statistics calculation step using STACKS pipeline. Existing *Gasterosteus aculeatus* draft genome will not be used here so the analysis will be performed de novo. In a de novo RAD-seq data analysis, the reads are aligned one on each other to create stacks and then clustered to build loci. A reference approach can also be conducted (see [ref_based tutorial]({{site.baseurl}}{% link topics/sequence-analysis/tutorials/ref-based-rad-seq/tutorial.md %}), allowing to work on existing assembled loci).
+We here proposed to re-analyze these data at least until the population genomics statistics calculation step using STACKS pipeline. Existing *Gasterosteus aculeatus* draft genome will not be used here so the analysis will be performed de novo. In a de novo RAD-seq data analysis, the reads are aligned one on each other to create stacks and then clustered to build loci. A reference approach can also be conducted (see [ref_based tutorial]({{site.baseurl}}{% link topics/ecology/tutorials/ref-based-rad-seq/tutorial.md %}), allowing to work on existing assembled loci).
 
 
 > ### Agenda

diff --git a/...kflows/Galaxy-Workflow-de-novo-rad-seq.ga → ...kflows/Galaxy-Workflow-de-novo-rad-seq.ga b/...kflows/Galaxy-Workflow-de-novo-rad-seq.ga → ...kflows/Galaxy-Workflow-de-novo-rad-seq.ga
diff --git a/...als/genetic-map-rad-seq/data-library.yaml → ...als/genetic-map-rad-seq/data-library.yaml b/...als/genetic-map-rad-seq/data-library.yaml → ...als/genetic-map-rad-seq/data-library.yaml
diff --git a/...rials/genetic-map-rad-seq/tours/tour.yaml → ...rials/genetic-map-rad-seq/tours/tour.yaml b/...rials/genetic-map-rad-seq/tours/tour.yaml → ...rials/genetic-map-rad-seq/tours/tour.yaml
diff --git a/...tutorials/genetic-map-rad-seq/tutorial.md → ...tutorials/genetic-map-rad-seq/tutorial.md b/...tutorials/genetic-map-rad-seq/tutorial.md → ...tutorials/genetic-map-rad-seq/tutorial.md
diff --git a/...-rad-seq/workflows/genetic-map-rad-seq.ga → ...-rad-seq/workflows/genetic-map-rad-seq.ga b/...-rad-seq/workflows/genetic-map-rad-seq.ga → ...-rad-seq/workflows/genetic-map-rad-seq.ga
diff --git a/...rials/ref-based-rad-seq/data-library.yaml → ...rials/ref-based-rad-seq/data-library.yaml b/...rials/ref-based-rad-seq/data-library.yaml → ...rials/ref-based-rad-seq/data-library.yaml
diff --git a/...torials/ref-based-rad-seq/tours/tour.yaml → ...torials/ref-based-rad-seq/tours/tour.yaml b/...torials/ref-based-rad-seq/tours/tour.yaml → ...torials/ref-based-rad-seq/tours/tour.yaml
diff --git a/...s/tutorials/ref-based-rad-seq/tutorial.md → ...y/tutorials/ref-based-rad-seq/tutorial.md b/...s/tutorials/ref-based-rad-seq/tutorial.md → ...y/tutorials/ref-based-rad-seq/tutorial.md
diff --git a/...lation_genomics_with_reference_genome_.ga → ...lation_genomics_with_reference_genome_.ga b/...lation_genomics_with_reference_genome_.ga → ...lation_genomics_with_reference_genome_.ga
diff --git a/...s/ref-based-rad-seq/workflows/workflow.ga → ...s/ref-based-rad-seq/workflows/workflow.ga b/...s/ref-based-rad-seq/workflows/workflow.ga → ...s/ref-based-rad-seq/workflows/workflow.ga
diff --git a/topics/sequence-analysis/images/Stacks_M_parameter_within_ind_dist.png b/topics/sequence-analysis/images/Stacks_M_parameter_within_ind_dist.png
diff --git a/topics/sequence-analysis/images/Stacks_components.png b/topics/sequence-analysis/images/Stacks_components.png
diff --git a/topics/sequence-analysis/images/Stacks_m_parameter_stack_depth.png b/topics/sequence-analysis/images/Stacks_m_parameter_stack_depth.png
diff --git a/topics/sequence-analysis/images/Stacks_pipelines.png b/topics/sequence-analysis/images/Stacks_pipelines.png