Select the Graphical Sequence View and see that the graphical view opens in a new tab (if the record has been updated you might see a warning message, click the OK button to close it). Double click on NT_ accession to open the Open View dialog. Now there is a 'New Project' in the Project Tree View. Click Next three times (skip mapping dialog, since this data has mapped already) and then click Finish. Navigate to the BAM Test Files folder you downloaded, select scenario1_with_index, select file and click Open. Select button on the right that says Add BAM/CSRA file. Step 2: BAM file with index fileįrom the File menu choose Open and select BAM/CSRA files from the left side. For more information please refer to the Displaying de-novo BAM files tutorial. 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. See this video for information about viewing BAM files on the web GDV browser (note, this data will not be secure). 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".
#Linux sequencher files install#
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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