Hi @abhi_g
Thanks for sharing the screenshot, very helpful!
Glad you have this all connected now! If you are not sure how to zoom into the details, try this:
Navigating IGV
- The first pull-down menu (to the immediate right of the “IGV hg38” text), choose a chromosome (instead of “all”).
- The second bar is free-text, and accepts coordinates.
- You can also click around the other functions on the display to zoom/scroll/group/highlight and more including how the display is presented.
IGV has a nice user guide for learning how to navigate. This is the section where the address bar is discussed. Online videos are another resource!
IGV User Guide → https://igv.org/doc/webapp/#UserGuide/#navigating-the-view
IGV should mostly work the same in Galaxy as it does when used directly but please let us know if something seems different, or if you simply need a tip, and we can help more here!
Screenshots
Note that I converted to a bigwig to create a coverage map that can be seen at more zoom levels!
Where are the bases? Toggle that track’s option to show!
BAM datatypes
I’ll also quickly mention that a distinct step to sort a bam dataset is Galaxy is usually not needed, which may save you time, steps, and duplicated data storage. Why? All bam datasets are coordinate sorted when they are initially created and indexed as a default action.
Inspecting the bam under the Raw tab will allow you to see this notation at the top of the header in the @HD line. It will look like this.
@HD VN:1.5 SO:coordinate
This indexing occurs during Upload or when a tool produces a bam output. The datatype bam is reserved for this, so whenever that is assigned, a coordinate sort can be safely assumed and the header can confirm.
When a bam dataset is unsorted (very rare), or numerically sorted (certain protocols), the dataset will be assigned a different reserved datatype. These are based on the header content so changing the datatype yourself isn’t recommended. Instead, allow tools to interpret the data and assign the appropriate type.
Detail: bam (SO:coordinate) and qname_sorted.bam (SO:queryname) are the two bam variations most people will encounter. Use coordinate sorted bam with IGV as a qname_sorted.bam can trigger a conversion that stays in the “loading dataset” stage until it eventually fails! This would happen outside of Galaxy too!
Hope this helps and please let us know how it goes! 