.. _radsex-usage: Usage ===== The RADSex software implements the general command-line interface: ``radsex [options]`` **Available commands** ======= =========== Command Description ======= =========== depth Compute marker depth statistics for each individual distrib Compute the distribution of markers between compared groups freq Compute the distribution of markers in all individuals map Align markers to a genome and compute metrics for each aligned marker process Compute a table of marker depths from a set of demultiplexed reads files signif Extract markers significantly associated with phenotypic group from a marker depths table subset Extract a subset of markers from a marker depths table ======= =========== ------------------------------------------------------------------------------------------------------------ .. _radsex-usage-process: process ------- Generate a table containing the depth of each marker in each individual from the dataset. **Command** :: radsex process --input-dir input_dir_path --output-file output_file_path [ --threads n_threads --min-depth min_depth ] **Options** ===================== =========== Option Description ===================== =========== ``--input-dir, -i`` Path to a folder containing demultiplexed reads ``--output-file, -o`` Path to the generated marker depths table ``--threads, -T`` Number of threads to use (default: 1) ``--min-depth, -d`` Minimum depth to consider a marker present in an individual (default: 1) ===================== =========== **Output** A :ref:`radsex-output-depth-table`: :: #Number of markers : 4 id sequence individual_1 individual_2 individual_3 individual_4 individual_5 0 TGCA..TATT 0 15 24 17 21 1 TGCA..GACC 20 18 3 26 4 2 TGCA..ATCG 2 1 5 16 0 3 TGCA..CCGA 14 29 23 2 19 .. note:: Input files are automatically dectected from the input directory based on their extensions. Supported extensions are **.fa**, **.fa.gz**, **.fq**, **.fq.gz**, **.fasta**, **.fasta.gz**, **.fastq**, **.fastq.gz**, **.fna**, and **.fna.gz**. Individual IDs in the output table will be inferred from the input files names after removing the extension. For instance, a file named **individual_1.fastq.gz** will be attributed the ID **individual_1**. Make sure to use the same IDs when creating the population map. ------------------------------------------------------------------------------------------------------------ .. _radsex-usage-distrib: distrib ------- Generate a table containing the distribution of markers between two groups of individuals defined in a :ref:`radsex-input-popmap`. **Command** :: radsex distrib --markers-table markers_table_path --output-file output_file_path --popmap popmap_path [ --min-depth min_depth --groups group1,group2 --signif-threshold signif_threshold --disable-correction ] **Options** ============================ =========== Option Description ============================ =========== ``--markers-table, -t`` Path to a marker depths table generated by "process" ``--popmap, -p`` Path to a tabulated file specifying groups for all individuals ``--output-file, -o`` Path to the output file (distribution of markers between groups) ``--min-depth, -d`` Minimum depth to consider a marker present in an individual ``--groups, -G`` Names of the groups to compare if there are more than two groups in the popmap (--groups group1, group2) ``--signif-threshold, -S`` P-value threshold to consider a marker significantly associated with a phenotypic group ``--disable-correction, -C`` If set, Bonferroni correction will NOT be used when assessing significance of association with phenotypic group ============================ =========== **Output** A :ref:`radsex-output-distrib`: :: Males Females Markers P CorrectedP Signif Bias 0 1 7 1 1 False -0.333 0 2 3 0.39 1 False -0.666 0 3 1 0.10 1 False -1.000 1 0 6 1 1 False 0.333 1 1 5 1 1 False 0.000 1 2 1 1 1 False -0.333 1 3 2 0.39 1 False -0.666 2 0 3 0.39 1 False 0.666 2 1 8 1 1 False 0.333 2 2 4 1 1 False 0.000 2 3 2 1 1 False -0.333 3 0 4 0.10 1 False 1.000 3 1 7 0.39 1 False 0.666 3 2 6 1 1 False 0.333 3 3 9 1 1 False 0.000 ------------------------------------------------------------------------------------------------------------ .. _radsex-usage-signif: signif ------ Find markers significantly associated with groups of individuals defined in a :ref:`radsex-input-popmap`. **Command** :: radsex signif --markers-table markers_table_path --output-file output_file_path --popmap popmap_path [ --min-depth min_depth --groups group1,group2 --signif-threshold signif_threshold --disable-correction --output-fasta ] **Options** ============================ =========== Option Description ============================ =========== ``--markers-table, -t`` Path to a marker depths table generated by "process" ``--popmap, -p`` Path to a tabulated file specifying groups for all individuals ``--output-file, -o`` Path to the output file (distribution of markers between groups) ``--min-depth, -d`` Minimum depth to consider a marker present in an individual ``--groups, -G`` Names of the groups to compare if there are more than two groups in the popmap (--groups group1, group2) ``--signif-threshold, -S`` P-value threshold to consider a marker significantly associated with a phenotypic group ``--disable-correction, -C`` If set, Bonferroni correction will NOT be used when assessing significance of association with phenotypic group ``--output-fasta, -a`` If set, markers are saved to a fasta file instead of a markers depth table ============================ =========== **Output** :ref:`radsex-output-depth-table`: :: #Number of markers : 4 id sequence individual_1 individual_2 individual_3 individual_4 individual_5 0 TGCA..TATT 0 15 24 17 21 1 TGCA..GACC 20 18 3 26 4 2 TGCA..ATCG 2 1 5 16 0 3 TGCA..CCGA 14 29 23 2 19 :ref:`radsex-output-fasta`: :: >4495827_F:0_M:21_p:1.14577e-07_pcorr:2.64584e-03_mindepth:10 TGCAG.....GGATGTGTATCCATA >4609394_F:0_M:23_p:1.08057e-08_pcorr:3.13548e-04_mindepth:10 TGCAG.....GGTTCCATCCCAAAT >4661391_F:0_M:26_p:1.92225e-10_pcorr:8.95316e-06_mindepth:10 TGCAG.....GTAGAGTGACCAGTT >5182569_F:0_M:22_p:3.62243e-08_pcorr:6.43275e-04_mindepth:10 TGCAG.....ACATGCTGTAAATGC >5625957_F:0_M:25_p:7.91633e-10_pcorr:1.16345e-06_mindepth:10 TGCAG.....CTGGAGAAGAGTAGG ------------------------------------------------------------------------------------------------------------ .. _radsex-usage-map: map --- Align markers to a genome and compute bias and probability of association with group for each aligned marker. **Command** :: radsex map --input-file input_file_path --output-file output_file_path --population-map popmap_file_path --genome-file genome_file_path [ --min-depth min_depth --min-quality min_quality --min-frequency min_frequency ] **Options** ============================ =========== Option Description ============================ =========== ``--markers-table, -t`` Path to a marker depths table generated by "process" ``--popmap, -p`` Path to a tabulated file specifying groups for all individuals ``--output-file, -o`` Path to the output file (distribution of markers between groups) ``--genome-file, -g`` Path to the genome file ``--min-depth, -d`` Minimum depth to consider a marker present in an individual ``--groups, -G`` Names of the groups to compare if there are more than two groups in the popmap (--groups group1, group2) ``--min-quality, -q`` Minimum mapping quality to retain a marker ``--min-frequency, -Q`` Minimum frequency of individuals in which a marker is present to retain a marker ``--signif-threshold, -S`` P-value threshold to consider a marker significantly associated with a phenotypic group ``--disable-correction, -C`` If set, Bonferroni correction will NOT be used when assessing significance of association with phenotypic group ============================ =========== **Output** A :ref:`radsex-output-map`: :: Contig Position Length Marker_id Bias P CorrectedP Signif LG03 18366992 36623554 4335174 -0.202 0.073 1 False LG05 28289991 33792114 4335919 0 1 1 False LG05 29738230 33792114 4336169 0.149 0.356 1 False LG22 71119 28810691 4336631 0.159 0.162 1 False LG15 20142338 30000224 4336732 0 1 1 False LG02 26668964 31118443 4337320 0 1 1 False LG03 4463700 36623554 4337383 -0.033 0.973 1 False LG13 32240045 33409148 4338936 -0.073 0.704 1 False LG13 19113343 33409148 4340342 0.064 0.479 1 False LG22 22503191 28810691 4341087 -0.080 0.704 1 False LG01 17881236 39973033 8678129 -0.736 1.112e-03 1 True LG01 16475480 39973033 8888270 -0.705 4.773e-03 1 True LG01 15761951 39973033 8954765 -0.769 2.629e-04 1 True LG01 16562550 39973033 8990122 -0.736 1.112e-03 1 True ------------------------------------------------------------------------------------------------------------ .. _radsex-usage-subset: subset ------ Extract a subset of markers from a markers depth table based on presence in individuals from each compared group. **Command** :: radsex subset --markers-table markers_table_path --output-file output_file_path --popmap popmap_path [ --min-depth min_depth --groups group1,group2 --signif-threshold signif_threshold --disable-correction --min-group1 min_group1 --min-group2 min_group2 --max-group1 max_group1 --max-group2 max_group2 --min-individuals min_individuals --max-individuals max_individuals --output-fasta ] **Options** ============================ =========== Option Description ============================ =========== ``--markers-table, -t`` Path to a marker depths table generated by "process" ``--popmap, -p`` Path to a tabulated file specifying groups for all individuals ``--output-file, -o`` Path to the output file (subset of markers) ``--min-depth, -d`` Minimum depth to consider a marker present in an individual ``--groups, -G`` Names of the groups to compare if there are more than two groups in the popmap (--groups group1, group2) ``--signif-threshold, -S`` P-value threshold to consider a marker significantly associated with a phenotypic group ``--disable-correction, -C`` If set, Bonferroni correction will NOT be used when assessing significance of association with phenotypic group ``--output-fasta, -a`` If set, markers are saved to a fasta file instead of a markers depth table ``--min-group1, -m`` Minimum number of individuals from the first group to retain a marker in the subset ``--min-group2, -n`` Minimum number of individuals from the second group to retain a marker in the subset ``--max-group1, -M`` Maximum number of individuals from the first group to retain a marker in the subset ``--max-group2, -N`` Maximum number of individuals from the second group to retain a marker in the subset ``--min-individuals, -i`` Minimum number of individuals to retain a marker in the subset ``--max-individuals, -I`` Maximum number of individuals to retain a marker in the subset ============================ =========== **Output** :ref:`radsex-output-depth-table`: :: #Number of markers : 4 id sequence individual_1 individual_2 individual_3 individual_4 individual_5 0 TGCA..TATT 0 15 24 17 21 1 TGCA..GACC 20 18 3 26 4 2 TGCA..ATCG 2 1 5 16 0 3 TGCA..CCGA 14 29 23 2 19 :ref:`radsex-output-fasta`: :: >4495827_F:0_M:21_p:1.14577e-07_pcorr:2.64584e-03_mindepth:10 TGCAG.....GGATGTGTATCCATA >4609394_F:0_M:23_p:1.08057e-08_pcorr:3.13548e-04_mindepth:10 TGCAG.....GGTTCCATCCCAAAT >4661391_F:0_M:26_p:1.92225e-10_pcorr:8.95316e-06_mindepth:10 TGCAG.....GTAGAGTGACCAGTT >5182569_F:0_M:22_p:3.62243e-08_pcorr:6.43275e-04_mindepth:10 TGCAG.....ACATGCTGTAAATGC >5625957_F:0_M:25_p:7.91633e-10_pcorr:1.16345e-06_mindepth:10 TGCAG.....CTGGAGAAGAGTAGG ------------------------------------------------------------------------------------------------------------ .. _radsex-usage-freq: freq ---- Generate a table containing the distribution of markers in the entire dataset. **Command** :: radsex freq --markers-table markers_table_path --output-file output_file_path [ --min-depth min_depth ] **Options** ============================ =========== Option Description ============================ =========== ``--markers-table, -t`` Path to a marker depths table generated by "process" ``--output-file, -o`` Path to the output file (distribution of markers between groups) ``--min-depth, -d`` Minimum depth to consider a marker present in an individual ============================ =========== **Output** A :ref:`radsex-output-freq`: :: Frequency Count 1 10389 2 3869 3 2884 4 1824 5 1672 6 1276 7 1261 8 1278 9 1355 10 1291 ------------------------------------------------------------------------------------------------------------ .. _radsex-usage-depth: depth ----- Compute the number of reads and markers as well as the minimum, maximum, median, and average marker depth in each individual from the dataset. **Command** :: radsex depth --markers-table markers_table_path --popmap popmap_file --output-file output_file_path **Options** ============================ =========== Option Description ============================ =========== ``--markers-table, -t`` Path to a marker depths table generated by "process" ``--popmap, -p`` Path to a tabulated file specifying groups for all individuals ``--output-file, -o`` Path to the output file (distribution of markers between groups) ``--min-depth, -d`` Minimum depth to consider a marker present in an individual ============================ =========== **Output** A :ref:`radsex-output-depth`: :: Individual Group Reads Markers Retained Min_depth Max_depth Median_depth Average_depth SRR1519834 M 3929067 669084 72938 0 60604 60 71 SRR1519837 M 6018684 963531 72938 0 48628 44 53 SRR1519830 F 4844480 818700 72938 0 35358 54 72 SRR1519853 M 3462244 502028 72938 0 27276 28 33 SRR1519824 F 3518348 604081 72938 0 23912 21 27 SRR1519819 F 3815684 622309 72938 0 36001 24 32 SRR1519846 M 4731003 758814 72938 0 30307 31 36 SRR1519829 F 6928277 909117 72938 0 64723 45 61 SRR1519812 F 7547724 1165312 72938 0 44358 36 46 SRR1519862 M 5948867 945346 72938 0 64356 69 81