Is there a way to check how many jobs a user has in the queue?

I think you're looking for the 'user' option of qstat. qstat -u username lists all jobs belonging to the given user. Wildcards can be included with a backslash: qstat -u \\* lists all jobs.

To answer your specific question (total jobs), you can use wc to count the lines that qstat outputs:

qstat -u username | wc -l

But that will give two more than the actual jobs because qstat has two header lines. So the full command you may want is:

expr $(qstat -u username | wc -l) - 2

Which asks for the jobs by user username, counts the numbers of lines, and subtracts 2.

Number of header lines may be different from 2 (e.g., on our Cray it is 5). Another solution is:

qselect -u username | wc -l

qselect does not produce header lines.