Quickstart for the impatient

If you know how to install python packages from PyPI and how to use the command line, you can follow the instructions in this section to get PacBio Data Processing up and running.

Alternatively, if you need a step-by-step guide to use PacBio Data Processing on a cluster, follow the Quickstart on a cluster guide.

Installation

To install PacBio Data Processing, open an interactive shell and run:

pip install PacBioDataProcessing

or, alternatively:

python -m pip install PacBioDataProcessing

Note

More details as well as alternative installation methods are explained in Installation.

Warning

Although the installation of PacBio Data Processing is now complete, there are some runtime dependencies. That means that they must be there before using PacBio Data Processing. See Other dependencies and the links therein for the list of dependencies and suggestions on how to install them.

Using PacBio Data Processing

To do a single molecule analysis of m6A methylations in DNA, you need:

  • a BAM file with the result of the sequencing, and

  • the reference file: a .fa/.fasta plus the companion .fa.fai/.fasta.fai file

and use the sm-analysis program, feeding it with those files.

For example, if the bam file’s name is mysequence.bam and the reference files are myreference.fasta and myreference.fasta.fai, then the sm-analysis program will carry out a single molecule analysis of the m6A methylations found during sequencing with the following command:

sm-analysis mysequence.bam myreference.fasta

In the Usage section you can find detailed information about the output and the possible input options available in sm-analysis as well as a description of other tools provided by this package (like bam-filter).