bax2bam wiki: installation, basic usage and FAQ

Armin Töpfer edited this page Jun 11, 2018 · 3 revisions


The tool bax2bam is provided via bioconda

conda install -c bioconda bax2bam

Basic usage

  • Convert a SMRTCell movie (which contain three bax.h5 files) to BAM.
bax2bam movie.1.bax.h5 movie.2.bax.h5 movie.3.bax.h5 -o movie --subread
  • Convert a SMRTCell movie to BAM and propagate additional pulse features (QVs).
bax2bam movie.1.bax.h5 movie.2.bax.h5 movie.3.bax.h5 -o movie --subread --pulsefeatures=DeletionQV,DeletionTag,InsertionQV,IPD,MergeQV,SubstitutionQV,PulseWidth,SubstitutionTag

Note that we recommend to convert a single SMRTCell (e.g., movie.1.bax.h5, movie.2.bax.h5 and movie.3.bax.h5) to a single BAM file. Converting multiple SMRTCells (e.g., movie1..bax.h5 and movie2..bax.h5) into a single BAM file is not recommended.


  • Why I observed 'ERROR: unsupported sequencing chemistry combination' and how to fix the issue? Most of time, seeing this error indicates that bam2bax cannot find movie.metadata.xml associated with the SMRTCell.

    Each SMRTCell must be associated with movie.metadata.xml which contains chemistry combination, and the movie.metadata.xml must be saved in the parent directory of movie.*.bax.h5 files, looking exactly like below,

    ├── Analysis_Results
    │   ├── m130802_062611_ethan_c100542982550000001823084811241306_s1_p0.1.bax.h5
    │   ├── m130802_062611_ethan_c100542982550000001823084811241306_s1_p0.2.bax.h5
    │   ├── m130802_062611_ethan_c100542982550000001823084811241306_s1_p0.3.bax.h5
    │   └── m130802_062611_ethan_c100542982550000001823084811241306_s1_p0.bas.h5
    └── m130802_062611_ethan_c100542982550000001823084811241306_s1_p0.metadata.xml

    This error can be fixed by simply copying movie.metadata.xml to where it should be located.

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