For more information on SRR run accessions of GenBank data (and ERR/DRR run accessions for data originating from EMBL-EBI/DDBJ correspondingly) see SRA knowledge base page. For more information on BAM files, see the BAM file FAQ section and Import BAMs video tutorial. To see an example for a BAM file from a remote (ftp) location, please check BAM haplotype filtering tutorial. Example files for this tutorial can be downloaded here (note the file is large ~356MB): 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. SRR13020989 – SRA run accession for data originated from GenBank.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. Step 5: BAM data for SRA run accessionsīAM files can be opened from remote locations (ftp, http) and from local computers.
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