rsem-calculate-expression : Problem using multiple paired-end FASTQ files

[Nik]

Hello:

Could you please help me. I am trying to run DE using the following pattern:

rsem-calculate-expression [options] --paired-end upstream_read_file(s) downstream_read_file(s) reference_name sample_name

but I get that the number of arguments is invalid. The 4 sets of paired reads that I am using are represented by 8 .fastq files, so what I run is:

rsem-calculate-expression --paired-end \

file1_R1_filtered.fastq, \

file2_R1_filtered.fastq, \

file3_R1_filtered.fastq, \

file4_R1_filtered.fastq \

file1_R2_filtered.fastq, \

file2_R2_filtered.fastq, \

file3_R2_filtered.fastq, \

file4_R2_filtered.fastq \

My_reference \

My_DE_Results

Thanks in advance,

Nik

[Colin Dewey]

Hi Nik,

You will need to make sure that there is no whitespace between the filenames of the fastq files of each set (upstream or downstream) of reads. Otherwise, RSEM thinks you are giving it too many arguments. Something like the following should work:

rsem-calculate-expression --paired-end \
file1_R1_filtered.fastq,file2_R1_filtered.fastq,file3_R1_filtered.fastq,file4_R1_filtered.fastq \
file1_R2_filtered.fastq,file2_R2_filtered.fastq,file3_R2_filtered.fastq,file4_R2_filtered.fastq \
My_reference \
My_DE_Results

Colin

[Nik]

Prof. Dewey:

Thank you, it worked.

Regards,
Nik