Importing BAM files into an Assembly Project

You can import BAM files, containing reads mapped against a reference sequence, into a MacVector Assembly Project. As well as the BAM file(s) you will also need the original reference sequence the reads were mapped against. FASTA is fine, but an annotated reference is better for visualisation.

The tool needed is called ADD CONTIG. This is one of the toolbar buttons in an Assembly Project:

First create a new assembly project.

  • FILE > NEW > ASSEMBLY PROJECT

  • click ADD REF to add the reference sequence.

  • Use ADD CONTIG to import your BAM/SAM file.

Then you need to associate the BAM file(s) with the reference:

– select the reference and an imported contig(BAM file).

  • Right click on and select UNITE REFERENCE WITH CONSENSUS SEQUENCE

You can optionally also generate a report on any variants (either at the previous step or a later stage).

  • Right Click and choose GENERATE VCF

If you import multiple BAM files against the same reference sequence you can also graphically compare these datasets with the Coverage Tab (third tab along in the Assembly Project window).

CoverageTabx2

Incidentally if you need to access the BAM files from within MacVector’s Assembly Projects then you can right click on an Assembly Project and view the contents.

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