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SortmeRNA facing error

Hello,
I am trying to use sortmeRNA to know the details about the RNA present in my sample. I am using sortmeRNA for this. When I try to use it, it gives me an error saying: "'d' is not one of the options". Whereas, my command does not have "d" or spaces between them. Please let me know where I am going wrong.
The command which I used is:

sortmerna --ref /dir/ref.fa,/dir/SAindex --reads R1.fq R2.fq --aligned output.sortedByCoord.out.bam --match --coverage

Thanks for your help in advance

error sortmerna rna-seq
• 2,571 views • link
updated by h.mon h.mon • written by Inquisitive8995 Inquisitive8995

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

• 1 views • link
written by Ram Ram

Thank you. I was not aware of that previously.

• 2 views • link
written by Inquisitive8995 Inquisitive8995

1 answer

SortMeRNA accepts only 1 file as input for the reads. If a user has two input files, in the case for the foward and reverse paired-end reads (see Figure 2), they may use the merge-paired-reads.sh script found in 'sortmerna/scripts' folder to interleave the paired reads

You are using --reads R1.fq R2.fq, which SortMeRNA doesn't handle.

• 1 views • link
written by h.mon h.mon

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