I'm a new PhD student and bioinformatics is all very new to me so apologies if this seems trivial. I have some paired-end RNA-seq data which I've managed to convert to sorted and indexed bam files however I'm confused to where I go from here, am I right in thinking I can now visualise this data and if so how? 
You can visualise the indexed BAMs with [IGV][1]. It should be pretty straight forward if you **choose the correct genome build**.

If you are working human or mouse genome, or any of the genomes listed on [ucsc genome browser][2], you can convert your bam files to bigwig files using [deepTools2][3] and create [tracks][4] to be viewed on genome browser. These tracks can be saved and visualised on any web browser and can be shared with collaborators.


  [1]: http://software.broadinstitute.org/software/igv/home
  [2]: https://genome-euro.ucsc.edu/cgi-bin/hgGateway?hgsid=602554305_kMaKYkyWlt61jjMmoBrR3w3UtOHA&redirect=manual&source=genome.ucsc.edu
  [3]: http://deeptools.readthedocs.io/en/latest/content/tools/bamCoverage.html
  [4]: https://genome.ucsc.edu/goldenpath/help/customTrack.html