How do I run a .fastq single-end file in rsem-calculate-expression?

Question

[matheusribalves]

The following command does not work:

rsem-calculate-expression --num-threads 8 --time --star --paired-end $fastq1 $fastq2 $(file_directory_output)

"Invalid number of arguments!"

Please does anyone have suggestions that might help me? Tks.

[ATpoint]

Hi, please read the manual, it is clearly explained how to run single-end files. https://deweylab.github.io/RSEM/rsem-calculate-expression.html

Answer 1

[svp]

Remove --paired-end from your command and run as follows:

rsem-calculate-expression --num-threads 8 --time --star $fastq $(file_directory_output)