I’m currently doing NGS data analysis for a biological research group. They would like to have files for visualisation in the USCS Genome Browser (they strongly prefer it over IGV). Unfortunately, the bigwig files I created directly from the sequencing .bam files were much too large to be loaded into the Browser (worked fine in IGV).
Therefore, the idea was to only include those reads that were part of a peak call (note that this visualisation is not intended to be included in any publication - it serves merely as visual validation for the experimenters).
Does anyone have an idea what the best approach would be? Is there maybe a tool that can achieve this efficiently? My own approach would have included conversion from .bam to .sam, then filtering on the .sam file (removing the reads that are not overlapped by a peak region), which is of course not only much too slow for a .sam file containing thousands of reads, but also takes up way too much server space.
Thanks in advance for any directions!
I kind of doubt you reached the limits of the browser as it can visualize tracks from large WGS data. Did you follow the intstructions on how to load bigwig (deposited on a publically-accessable server and providing the URL to UCSC browser)?
concat : If you are unable to host the bigwig files on an externally accessible website then you could always install a local mirror of UCSC browser.
Thanks for both of your answers! I will look into the local mirror solution by genomax, as it is indeed a problem that the department I'm working in currently has no access to/permission for using the publically available institute server. While access can be requested, this would take some time, so I wanted to know if there was a quicker way around using it that I could do on my own. I will report back as soon as I have tried it!
Update: We now loaded the .narrowPeak files into the Browser, showing only the regions of significant enrichment. This is just the pilot data of the study, so it will suffice for the moment. Once all the data has arrived, we will request access to the public server and visualise the complete read enrichment.