Running Read Mapping Analyses

The key features to a read mapping command are to supply the input read data along with any pairing information, the reference sequences, and the output file name.

A basic example of a read mapping command is the following: 

clc_mapper -o assembly.cas -d human.gb -q reads1.fasta reads2.fasta

The `-d' option indicates that the following files contain reference sequences and the `-q' option indicates that the following files contain read sequences. Both of these options may be used repeatedly. For example: 

clc_mapper -o assembly.cas -d human.gb -q reads1.fasta reads2.fasta
                                                         -d mito.gb

This command assembles the reads in the files read1.fasta and read2.fasta to the references sequences in the two files human.gb and mito.gb. The assembly may be done on one read file at a time and then later joined using the clc_join_mappings program.

For paired data, reads can be input either as single file where reads are interleaved or as two files which are automatically interleaved. In the following example paired reads are input as a single file: 

clc_mapper -o assembly.cas -d human.gb -q -p fb ss 180 250 joint.fasta

In the next example, paired reads are input as two files using the -i option: The above command would be identical to the following command, if the same paired data were in an interleaved file. 

{ \footnotesize
\begin{verbatim}
clc_mapper -o assembly.cas -d human.gb -q -p fb ss 180 250
                                                    -i first.fasta second.fasta

The above command would be identical to the following command, if the same paired data was in an interleaved file.

Please refer to the section on paired data input earlier in the manual for further details about that topic.

You can save index files for a reference set and then use the index file directly, instead of the reference sequence, in subsequent mappings.

Save the reference index: 

clc_mapper -o assembly.cas -d human.gb -q -p fb ss 180 250
                              joint.fasta  -n human-reference.index

Use the reference index: 

clc_mapper -o assembly.cas -d human-reference.index
                                      -q -p fb ss 180 250 joint.fasta

Further details are provided in Options for All Programs.