Input files

Reads files

RADSex accepts demultiplexed reads files as input for process. RADSex should work with any demultiplexed RAD-sequencing reads files regardless of technology (single / double digest) or enzyme. RADSex cannot support paired-end reads because insert sizes are variable, and thus the second read in a pair does not cover a consistent region of the genome.

Input files can be in fasta or fastq formats and can be compressed with gzip. RADSex uses file extensions to detect input files and supports the following extensions: .fa, .fa.gz, .fq, .fq.gz, .fasta, .fasta.gz, .fastq, .fastq.gz, .fna, and .fna.gz.

Individual IDs are inferred from file names, e.g. RADSex will attribute the ID individual_1 to the reads file individual_1.fastq.gz.

Group info

A group info file (or population map) is a headerless TSV file (i.e. a tabulated file using “\t” - the “tab” character - as a separator) with individual ID in the first column and group in the second column. Groups can be any value and there can be more than two groups. However, most radsex analyses compare metrics between two groups; if the groups info file contains more than two groups, you will have to specify the groups to compare with the --groups parameters (e.g. --groups males,females). If the popmap contains two groups, these groups will be used for group comparisons in their order of occurrence in the groups info file (this order can be overridden with --groups).

An example of population map is given below:

individual_1    M
individual_2    M
individual_3    F
individual_4    N
individual_5    F

Individual IDs can be any value, but it is important that they correspond to the name of the demultiplexed files (without the extension). For instance, the reads file for individual_1 should be named individual_1.fastq.gz (or any fasta/fastq format supported by your demultiplexer).

If you are using Stacks with a barcodes file to demultiplexing the RAD-sequencing reads, just make sure that individual IDs in the barcodes file and in the group info file are the same.

Chromosomes file

Genome-wide results from the map command are visualized using the radsex_map_circos(), radsex_map_manhattan(), and radsex_map_region() functions of sgtr. These function automatically identify contigs as chromosomes if their name starts with “LG”, “CHR”, or “NC” (case unsensitive). If this is not the case, or if you would like to rename the chromosomes (for instance to shorten NCBI “NC_XXX” IDs), you should provide a chromosomes names file to these functions.

The chromosomes names file is a headerless tabulated file with chromosome ID (from the genome file, e.g. “NC_XXXX”) in the first column and corresponding chromosome name in the second column (e.g. “Chrom1”).

An example of chromosomes names file is given below for the Northern Pike genome.

NC_025968.3     LG01
NC_025969.3     LG02
NC_025970.3     LG03
NC_025971.3     LG04
NC_025972.3     LG05
NC_025973.3     LG06
NC_025974.3     LG07
NC_025975.3     LG08
NC_025976.3     LG09
NC_025977.3     LG10
NC_025978.3     LG11
NC_025979.3     LG12
NC_025980.3     LG13
NC_025981.3     LG14
NC_025982.3     LG15
NC_025983.3     LG16
NC_025984.3     LG17
NC_025985.3     LG18
NC_025986.3     LG19
NC_025987.3     LG20
NC_025988.3     LG21
NC_025989.3     LG22
NC_025990.3     LG23
NC_025991.3     LG24
NC_025992.3     LG25

Note

Any scaffold included in the chromosomes names file will be considered a chromosome to be plotted as a sector. In most NCBI genomes, mitochondria are also named NC_XXX. As mitochondria are usually too small to be included as a sector in the circos plot, you should not add them to the chromosomes names file.