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

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.

RNA-Seq RSEM SRA rsem-calculate-expression RIBEIRO • 1.3k views
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Entering edit mode

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

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19 months ago
svp ▴ 450

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

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