![]() Thus, if you are working with a track-based read mapping, you can just use that alongside your original track-based reference genome sequence, for example, in a Track List.Įxtra notes on working with tracks within the Workbench: The genome sequence information in the original track set is the same as that in the stand-alone Sequence List you created. ![]() You do not need to convert your reference set back to track format if you started with a set of references in track format. More information about this is provided in the link below: (You can choose to create a track-based or stand-alone read mapping during this import). Import the SAM/BAM file using the reference set with the names that match those used in the SAM/BAM file.In the image below, we change the names from R to chrR (e.g. Use the Rename Sequences in Lists functionality ( ) from the Utility Tools folder in the Toolbox to change the names appropriately.If working with more than a few sequences:.Just right click on each sequence name in turn and choose the option Rename Sequence. If working with only a few sequences, you can change the names directly in the Sequence List.Instructions on how to do this is provided in the link below: Convert the reference genome sequence track to a stand-alone sequence list if the references are initially in track format.If you have a set of reference sequences in the Workbench that use one naming sequence and your SAM/BAM file contains references using a different naming scheme, then the method below can be used to create a reference set that can be used for importing the mapping data. For example, in the case of the human genome, chromosomes in different public resources have different naming patterns, such as "chrR", "R" and "NC_00000R", where R is some integer number or a letter. The issue of reference names commonly arises when using data from resources where different naming schemes are applied. If the reference names in a SAM/BAM file do not match the reference names in the Workbench, then the easiest route is usually to change names of the reference sequences in the Workbench to match those in your SAM/BAM file. The reference sequences in the SAM/BAM file and in the Workbench must match in both name and lengths in order to be able to import mapped data. To import mapping data from a SAM or BAM file you need to already have the reference sequences in the Workbench. This FAQ covers guidelines on how to import SAM/BAM file whose reference names are different than those present in the Workbench First-time users of CLC Gx on our workstation computers must complete the Workstation Request Form.How can I import mappings from a SAM/BAM file where the reference names are different to those in the Workbench?.All USC users can freely access the software on our workstation computers.Equipped with dual-CPU and 512GB RAM, one of our workstation computers is configured specifically to handle large data set and computationally intensive tasks such as de novo genome assembly and sequencing alignment.Wilson Dental Library, the University Park Campus.Norris Medical Library (RM203A), the Health Sciences Campus.The software has been installed on multiple workstation computers:.On workstation computers in the libraries.Mandatory registration is required for installing CLC Gx on your computer. Please submit the Local Installation Request Form.The computer must be connected to the USC network, either via Ethernet cable on campus or via USC VPN when using wireless (applies to both on- and off-campus wireless connections).Minimum hardware requirement for de novo assembly, metagenomics, and raw reads alignment:: 32GB RAM and Intel i7-6700 or faster processor.Minimum hardware requirement for general use: 16GB RAM and Intel i7-2600 or faster processor.The license consists of TWO concurrent user seats. USC has licensed CLC Gx for the free use of USC faculty, students and staff. ![]()
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