Welcome to the Genome Toolbox! I am glad you navigated to the blog and hope you find the contents useful and insightful for your genomic needs. If you find any of the entries particularly helpful, be sure to click the +1 button on the bottom of the post and share with your colleagues. Your input is encouraged, so if you have comments or are aware of more efficient tools not included in a post, I would love to hear from you. Enjoy your time browsing through the Toolbox.
Tuesday, November 19, 2013
Encode Features with no Strand Information in UCSC BED Format
The UCSC Genome Browser is a powerful tool that allows you to visualize your own data in custom tracks with respect to scores of other publicly available data tracks. To use some of the more advanced features for plotting .bed files, strand information is a required field in the .bed files. Usually, I would just arbitrarily assign a "+" for the strand information to indicate the feature was on the plus strand, when in actuality there is no relevant strand for the feature. This results in arrows (>>>>>>) being drawn over the feature in Genome Browser, not the end of the world, but still not the polished look I was going for. To circumvent this, I tried to leave the field blank when uploading a custom track, however, I would get the error: "Error line 1 of custom track: Expecting + or - in strand". Then I stumbled on a simple fix, that doesn't seem to be documented well. All Genome Browser needs is a period (.) in the strand field of the .bam file for each feature and all seems to work fine. The result: a sharp looking feature track in Genome Browser.