The usage and help documentation of
concoct_coverage_table.py can be seen by
usage: - [-h] [--samplenames SAMPLENAMES] bedfile bamfiles [bamfiles ...] A script to generate the input coverage table for CONCOCT using a BEDFile. Output is written to stdout. The BEDFile defines the regions used as subcontigs for concoct. This makes it possible to get the coverage for subcontigs without specifically mapping reads against the subcontigs. @author: inodb, alneberg positional arguments: bedfile Contigs BEDFile with four columns representing: 'Contig ID, Start Position, End Position and SubContig ID' respectively. The Subcontig ID must contain the pattern 'concoct_part_[0-9]*' while the contigs which are not cutup cannot contain this pattern. This file can be generated by the cut_up_fasta.py script. bamfiles BAM files with mappings to the original contigs. optional arguments: -h, --help show this help message and exit --samplenames SAMPLENAMES File with sample names, one line each. Should be same nr of bamfiles. Default sample names used are the file names of the bamfiles, excluding the file extension.
An example of how to run
concoct_coverage_table.py contigs_10K.bed mapping/Sample*.sorted.bam > coverage_table.tsv
This creates a coverage table suitable as input for concoct as the coverage_file parameter.
contigs_10K.bed file is created from the
cut_up_fasta.py script and the
bam-files needs to be sorted and indexed.