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Created with Raphaël 2.2.025Feb20Merge branch 'thimo.schotman-main-patch-39819' into 'main'mainmainUpdate metafiles/metadata_microbes_in_captivity.xlsxUpload New FileUpdate README.mdUpdate count_tables/filtered/filtered_precise_counts.txt, count_tables/filtered/filtered_raw_counts_cocult.txt, count_tables/filtered/filtered_raw_counts_meta.txt, count_tables/filtered/filtered_raw_counts_mono.txt, count_tables/filtered/filtered_raw_counts_precise_val.txt, count_tables/filtered/filtered_raw_precise_clean.txt, count_tables/original/raw_counts_meta.txt, count_tables/original/raw_counts_cocult.txt, count_tables/original/raw_counts_precise_val.txt, count_tables/original/raw_counts_mono.txt, count_tables/original/precise_counts.txt, count_tables/original/raw_precise_clean.txt, count_tables_log_tpm/filtered/filtered_log_tpm_precise_val.txt, count_tables_log_tpm/filtered/filtered_log_tpm_cocult.txt, count_tables_log_tpm/filtered/filtered_log_tpm_meta.txt, count_tables_log_tpm/filtered/filtered_log_tpm_mono.txt, count_tables_log_tpm/filtered/filtered_log_tpm_precise.txt, count_tables_log_tpm/filtered/filtered_log_tpm_precise_clean.txt, count_tables_log_tpm/normalized_419/log_tpm_419_precise_val.txt, count_tables_log_tpm/normalized_419/log_tpm_419_cocult.txt, count_tables_log_tpm/normalized_419/log_tpm_419_meta.txt, count_tables_log_tpm/normalized_419/log_tpm_419_mono.txt, count_tables_log_tpm/normalized_419/log_tpm_419_precise.txt, count_tables_log_tpm/original/log_tpm_meta.txt, count_tables_log_tpm/original/log_tpm_precise_val.txt, count_tables_log_tpm/original/log_tpm_mono.txt, count_tables_log_tpm/original/log_tpm_cocult.txt, count_tables_log_tpm/original/log_tpm_precise_clean.txt, count_tables_log_tpm/original/log_tpm_precise.txtUpdate scripts_analysis/accession_downloader.py, scripts_analysis/adding_count_tables.py, scripts_analysis/adjusting_genome_annotation_coordinates.py, scripts_analysis/bowtie_cocult.py, scripts_analysis/bowtie_mono.py, scripts_analysis/count_homology_validation.py, scripts_analysis/count_table_homology_normalization.py, scripts_analysis/counts_pantools_homology_groups.py, scripts_analysis/creating_bed_files.py, scripts_analysis/creating_log_tpm_counts.py, scripts_analysis/crossmapping_analysis.py, scripts_analysis/downloading_ftp.py, scripts_analysis/feature_counts.py, scripts_analysis/feature_counts_meta.py, scripts_analysis/feature_counts_mono.py, scripts_analysis/filtering_count_files_homology.py, scripts_analysis/filtering_count_tables_homology.py, scripts_analysis/mapping_pantools.py, scripts_analysis/mapping_verification_pantools.py, scripts_analysis/metatranscriptomics_quality.py, scripts_analysis/quality_check.py, scripts_analysis/read_direction.py, scripts_analysis/read_direction_meta.py, scripts_analysis/sorting_sam_files.py, scripts_pipeline/counts_pca.R, scripts_pipeline/normalization_visualisation.R, scripts_pipeline/precise_verification_correlation.R, scripts_pipeline/precise_verification_correlation_single.R, scripts_pipeline/raw_counts_vs_normalized_counts_scatterplots.R, scripts_pipeline/umap_and_tsne.R, metafiles/accessions_monocultures.txt, metafiles/accessions_precise_check.txt, metafiles/exemplar_genomes.txt, metafiles/map_list_verification.txt, metafiles/mapping_metadata.txt, metafiles/pan_gff_files.txt, metafiles/pan_metadata.txt, metafiles/pantools_map_list.txt, metafiles/pantools_verification_precise.txt, metafiles/srr_precise_id.txt, metafiles/ftp_links.txt, metafiles/metadata_precise.tsv, metafiles/pantools_homology_groups.txtUpload New FileAdding a new directory to store the metafiles and other useful files for the projectAdding new directory to store the scripts for the statistical analysis as performed in my thesisAdding the directory which will contain all the scripts to run the pipeline with.Initial commit