A unsorted BAM file with no index file (requires SAMTools). This tutorial will take you through several scenarios to view BAM files in Genome Workbench: To find aligned data, search the SRA database with a query that includes the parameter “aligned data", for example: ((("mus musculus") AND BALB/c ) AND "lymph") AND "rna seq" AND “aligned data". If there is no index file, you can use SAMTools to create one (please download SAMTools from and install locally).īAM data that is aligned to an assembly can be viewed as run accessions from the SRA database. The index should be named by appending “. For viewing BAM files, an index file must be found in the same directory as the BAM file.
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