Map_tax

Type motus map_tax to print the map_tax options.

OPTIONS:

• -f (FILE), input file(s) for reads in forward orientation, fastq formatted. The file(s) can also be a ZIP file (.gz or .bz2)
• -r (FILE), input file(s) for reads in reverse orientation, fastq formatted. The file(s) can also be a ZIP file (.gz or .bz2) example for forward and reverse reads analyzed in one lane:

motus map_tax -f for_sample.fastq -r rev_sample.fastq > sample.sam

example for forward and reverse reads analyzed in two lanes:

motus map_tax -f for_sample_lane1.fq,for_sample_lane2.fq -r rev_sample_lane1.fq,rev_sample_lane2.fq > sample.sam

Note that it is important that the files have the same order.

• -s (FILE), input file(s) for reads without mate, fastq formatted. The file(s) can also be a ZIP file (.gz or .bz2) You can analyze single read files alone:

motus map_tax -s sample_lane1.fq,sample_lane2.fq > sample.sam

or together with forward and reverse reads:

motus map_tax -f for_sample_lane1.fq,for_sample_lane2.fq -r rev_sample_lane1.fq,rev_sample_lane2.fq -s sample_lane1.fq > sample.sam

Note that in this last example we have only one single read for lane 1 and two lanes for for and rev, and this is not an error.

• -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 map_tax -s sample.fq > sample.sam
motus map_tax -s sample.fq -o sample.sam

• -t (INT), number of threads to use when running bwa. It is suggested to use multiple threads, so that bwa will run faster.
• -v (INT), verbose level: 1=error, 2=warning, 3=message, 4+=debugging. The default value is 3.
• -b, save the result of bwa in bam format. example to produce a sam file:

motus map_tax -s sample.fq > sample.sam

example to produce a bam file:

motus map_tax -s sample.fq -b > sample.bam

• -l, minimum length of alignment for the reads (number of nucleotides). Default value is 75.