I have BAM files of reads mapped to multiple different reference sequences within the one file. Is there an alignment viewer that would allow me to view those alignments at the same time on one screen? It would be also beneficial if I could view multiple BAM files that have multiple different reference sequences within each one at the same time too (perhaps in different windows) but this would just be a bonus - for me the most important thing is just to simultaneously view all the alignments stored within one BAM file.
I am currently using Tablet to view alignments however with Tablet you can only view each alignment within a single BAM file individually.
I'm sorry if this question has been answered before but I couldn't find a post that answered this for me.
Thank you for your help.