How do I add a BAM file to my computer?
From the File menu, choose Open and select BAM files from the left side of the dialog. Select button on the right that says Add a BAM file. Navigate to the BAM Test Files folder you have downloaded, select scenario2_no_index_unsorted_need_id_mapping and file GSM409307_UCSD.H3K4me1.bam, and click Next.
Where to find SAMtools in Bam test files?
Navigate to the BAM Test Files folder you have downloaded, select scenario2_no_index_unsorted_need_id_mapping and file GSM409307_UCSD.H3K4me1.bam, and click Next. You will see the dialog shown where Genome Workbench will ask where to find the SAMTools executable.
Where do I find the index file for BAM?
For viewing BAM files, an index file must be found in the same directory as the BAM file. The index should be named by appending “ .bai ” to the BAM file name. If there is no index file, you can use SAMTools to create one (please download SAMTools from http://samtools.sourceforge.net and install locally).
How is the map assembly function used in Bam?
If the BAM file uses a different style of sequence identifiers, the map assembly function allows Genome Workbench to convert them into NCBI assembly identifiers. This example requires mapping, since reference accessions in the bam file are not typical CenBank/RefSeq accessions.
How big is an example of BAM file?
Since BAM files can be VERY large, they are not loaded entirely into the Genome Workbench project as other types of data and are accessed externally. Example files for this tutorial can be downloaded here (note the file is large ~356MB):
How to display a de novo BAM file?
If you want to display de-novo BAM files that are aligned to novel (non-NCBI) genomes, you will need to first import a FASTA file with the sequences referred to in the BAM file and then import BAM file into the same project. For more information please refer to the Displaying de-novo BAM files tutorial.
https://www.youtube.com/watch?v=_aDOsDqm7ks