I would like to know if is possible to add BAM files from symbolic links (aka soft links).
To answer your question from a Unix perspective: GenomeBrowse will see the file system like any other application and symbolic links are handled by the OS to look like the files they soft link to.
As long as the .bam and .bam.bai file are still side-by-side it shouldn't matter if they are being read through a symbolic link.
In fact, I use this quite a lot when testing etc.
GenomeBrowse has built in file path linking functionality. By clicking the Add button on the main window of GenomeBrowse you can open the Add Data Sources dialog. On the bottom right corner click the button to Add/Remove Watched Folders and click the Add Path button under Additional Local Sources.
Browse to where the symbolic link is pointing to add that location to your Local folder directory. You will then be able to click on the available BAM files in this location to add them for visualization. If the symbolic link changes you will need to manually update the watched path as GenomeBrowse is unable to read the link directly.
Please let me know if you have any further questions.
Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.
Asked: 2014-02-26 08:08:42 -0600
Seen: 38 times
Last updated: Mar 20 '14