One-Step Mapping: the runMapping Command

2.15.2

If all the reads to be mapped to the reference sequence are available at once, the GS Reference Mapper application can process them with a single command, which has the following command line structure:

runMapping [options] refdesc [MIDList@]filedesc…

…where:

•	“[options]” are zero or more of the command line options (listed below),

•	the “refdesc” is one of the following:

◦	reffasta – a FASTA file containing the reference sequence(s),

◦	refdirname – a name or path for a directory containing the reference sequence (all FASTA files in the directory will be used as the reference),

◦	refgenome – a GoldenPath genome name (see the fourth Note, below),

•	–ref (reffasta \| refdirname)… -read

•	the string “-ref”, followed by multiple FASTA file names or directories, followed by the string “-read” (to mark the beginning of the read data files).

These options are order-dependent: -ref must be used prior to ‑reads.

•	each “filedesc” is one of the following:

◦	sfffilename or

◦	[regionlist:]datadir or

◦	readfastafile

•

and each “MIDList” is a multiplexing information string used to filter the set of file reads to be used in the mapping (see section 4.7 for the format of the MIDList information). If MIDs were used in the generation of the data file, then an MIDList string must be specified in order for the GS Reference Mapper to properly handle the file’s reads.

The runMapping command is actually a wrapper program around the newMapping and related commands used in incremental mapping (see section 2.15.3). After the incremental mapping command is completed, runMapping then transforms the project files and folders into this one-step form (which more closely matches the output structure of older versions of the “Mapping” application). The actions taken are:

•	All the mapping output files are moved up from the mapping sub-directory into the main folder

•	All internal data files in the mapping sub-directory are deleted

•	The 454MappingProject.xml and 454Project.xml files are deleted

•	The mapping sub-directory is deleted

If the –nrm option is given, runMapping does not perform this transformation, and the resulting folder can be used for further project-based mapping (the structure of the files/folders will match that of an incremental mapping project).

For data generated on the GS FLX+ System: The path given for any of the data directories may be prepended with an optional list of regions, separated from the path by a colon. For example:

1-3,4,6-8:D_yyyy_mm_dd_hh_min_sec_testuser_SignalProcessing

The list of regions must have the following format:

•	It must be a comma-separated list, ending with a colon.

•	Each element of the list can either be a single region number or a dash-separated range of region numbers.

•	Duplicate regions may be specified, and the regions may be specified in any order, but duplicates will be removed and the regions will be processed and reported in numerical order.

•	No spaces or other characters are allowed in the string.

If the region list is not present for a data directory path, all regions of the Run for that directory will be used in the mapping.

Any combination of explicit SFF files and data directory paths (with optional region lists) may be specified on the command line. For each data directory path given, the runMapping command will read the existing SFF files in the “sff” sub-directory of the data directory. If SFF files are not present in a data directory (e.g. for a Run whose data has been processed with a version of the 454 Sequencing System software anterior to 1.0.52), the signal processing step of the GS Run Processor application must be rerun on the Data Processing folder.

The path for any filename or data directory name can also be prepended with a multiplexing information string. Section 4.7 gives further information on using MIDs.

The data analysis software installation contains a default MID configuration file, found by default at Installation_path/454/config/MIDConfig.parse. This file is read by the GS Reference Mapper and used to match MID set names and MID names with their multiplexing information. Users can edit this file to add their own MID sets (following the format and syntax described in the file), or can copy this file to create their own separate MID configuration file (and then use the “-mcf” option to specify that as the MID configuration file to be used).

Contrary to the situation with incremental mapping (see the setRef command, section 2.15.3.2), you can use only one reference FASTA file, directory or GoldenPath genome name with the runMapping command, unless the –ref/-read options are included to separate the reference files from the read data files. All the files can still contain multiple reference sequences.

The GS Reference Mapper is aware of the folder/file structure of the UCSC GoldenPath genome databases (most specifically the human genome and the other major eukaryotic genome databases). If one or more of those databases are downloaded onto the DataRig, and the user sets a GOLDENPATH environment variable to the root directory containing those databases, then the genome name can be given as the reference for runMapping (i.e., the command “runMapping hg18 reads.sff” will map reads.sff against the GoldenPath hg18 human genome). The GS Reference Mapper will automatically read the chromosome FASTA files, the gene annotation file and the known SNP information file.

When given a GoldenPath genome (in genome mapping mode only, not for cDNA mapping), only the main chromosome files will be used as the reference by default. The GS Reference Mapper will not read the additional “_random” or “_hap” files contained in the chromosome directory. In order to include the “_random” and “_hap” files, the “-random” option must be given to the “setRef” or “runMapping” command.

Specifically, the Mapping application looks for the reference FASTA files in the “chromosomes” sub-directory, and files named “refGene.txt” and “snp###.txt” (i.e., a file like “snp130.txt” that begins with “snp”, has three digits, then ends with “.txt”) in the “database” sub-directory. This matches the organization of the human genome database. Other GoldenPath databases (which don’t match this organization) can be used by the GS Reference Mapper application if the files are modified to match this organization. See the UCSC GoldenPath “Downloads” page for information on how their genome databases can be downloaded (http://hgdownload.cse.ucsc.edu/downloads.html).

In addition to automatically reading the gene/coding-region annotation and known SNP files when the reference is a GoldenPath genome, the GS Reference Mapper application automatically searches for specific annotation/SNP files for any reference. If the reference files are located in a directory named “chromosomes”, the GS Reference Mapper will look for refGene.txt and snp###.txt files in a neighboring “database” directory (inside the same parent directory as “chromosomes”). The GS Reference Mapper also searches the same directory as the reference FASTA files for a refGene.txt and “snp###.txt”. Finally, if the reference consists of a single FASTA file, then the software will look for files with “.refGene” and “.snp” suffixes (e.g., if the reference file is “mygenome.fna”, then files “mygenome.refGene” and “mygenome.snp” will be tried.

To disable this automated reading of the annotation/SNP files, the ‑noannot and ‑nosnp options must be included as part of the command line options.