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
).