When using RSEM, I came across the error "Invalid number of arguments." Not sure where this arose from, since I separated the upstream and downstream reads with commas.
Usage: rsem-calculate-expression [options] --paired-end upstream_read_file(s) downstream_read_file(s) reference_name sample_name
My Code: /u/local/apps/RSEM/1.3.3/gcc-4.9.3/bin/rsem-calculate-expression --paired-end /u/project/run434_1.fastq, /u/project/run434_2.fastq, /u/project/run437_1.fastq, /u/project/run434_T_1.fastq, /u/project/run434_T_2.fastq, /u/project/run437_T_1.fastq Aet_ref Aet_samp
Aet_ref is the reference name, and Aet_samp is the sample name. Let me know what I can do to resolve this issue! Thank you!