Calc_mgc

Type motus calc_mgc to print the calc_mgc options.

OPTIONS:

• -i (FILE), provide a sam or bam input file(s), that you created before with map_tax. example:

motus calc_mgc -i sample.bam > mgc_reads.count

You can also submit a list of SAM/BAM file:

motus calc_mgc -i sample1_lane1.bam,sample1_lane2.sam > mgc_reads.count

Note the the program recognize automatically the file extension (bam or sam).

• -n (STR), name of the sample
• -o (FILE), output file name, if you don't provide any file than it will print in stdout. This two calls produce the same result:

motus calc_mgc -i sample.bam > mgc_reads.count
motus calc_mgc -i sample.bam -o mgc_reads.count

• -v (INT), verbose level: 1=error, 2=warning, 3=message, 4+=debugging. The default value is 3.
• -y (STR), type of read counts that we use. Possible values: [base.coverage, insert.raw_counts, insert.scaled_counts].
• -l, minimum length of alignment for the reads (number of nucleotides). Default value is 75.