Check multi-read mapping
From Array Suite Wiki
If you want to find how a specified multi-read is mapped, the best way is to work on the BAM or SAM file.
Genome Browser does not provide the read-filter, so we can only use it to infer how the multi-read is mapped by following steps:
Step 1. Browser -> Track -> Full Text Search Settings. Telling Array Studio that you want to search the information in the BAM file.
Step 2. Choose the samples. Note that when you choose multiple samples, or each sample has large number of reads, it may take some time to let the software finish the indexing.
Step3. Input the read name in the searching blank.
Step 4. A window would pop out showing that there are several mapping position found for this read.
In this case, there are 3 mapping locations found for this read. Note that for the uniquely mapped read, there should be 2 locations (pair-ended).
However, Genome Browser can only show you the region and all the reads in that region will be listed. It cannot only show you the read you’re interested in.
The region may look like this:
To better find out the multi-read in this region, there is one more thing we can do: just showing the reads that are multi-mapped. Select the track properties-> pileup-> Tag filter, input NH:i:2. If the read is uniquely mapped, the corresponding Tag is NH:i:1, otherwise the read is a multi-read, so you can try NH:i:2 or NH:i:3 and so on.