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

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
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updated by svp svp • written by matheusribalves • matheusribalves

1 answer

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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written by svp svp

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