concoct_coverage_table.py¶
Usage¶
The usage and help documentation of concoct_coverage_table.py
can be seen by
running concoct_coverage_table.py -h
:
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.
Example¶
An example of how to run concoct_coverage_table.py
:
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.
The contigs_10K.bed
file is created from the cut_up_fasta.py
script and the bam
-files needs to be sorted and indexed.