Contents
How to add a graph to a BAM file?
The steps for this part are identical to Steps 1 and 2 in this tutorial, however with a different data file. From the File menu choose Open and select BAM files from the left side. Select button on the right that says Add a BAM file. Navigate to the BAM Test Files folder you downloaded select with_index_with_graph.
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.
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 are SAM / BAM / CRAM files generated?
CRAM/unaligned Bam (uBAM) can be a source of data delivery in some institutions: this cuts down significantly on storage space and transfer speed. How are these files generated? Let’s look at one! The default tool for interacting with these formats is samtools.
Which is the best tool to work with BAM files?
Pointing a mouse to an individual alignment feature will open a tooltip with a lot of useful information about the alignment, including the CIGAR string, percent identity, and coverage. This exercise requires the use of SAMTools, a freely available package for working with BAM files.
How do I export an alignment table in Bam?
From the Graphical Sequence Viewer, zoom to the desired location and select a range of interest. Right-click the selected range and click the Export Data option in the context menu. An alignment export menu will be opened. Note that BAM files are stored as alignments, so you need to select “ Alignment Table File ” in the list on the left.
Is the BAM format the same as the Cram format?
This is a relatively new format that is very similar to BAM as it also retains the same information as SAM and is compressed, but it is much smarter in the way that it stores the information. It’s very interesting and up and coming but is a bit beyond the scope of this course.
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 big are BAM files in genome Workbench?
This tutorial will take you through several scenarios to view BAM files in Genome Workbench: 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.