SortmeRNA facing error

Question

[Inquisitive8995]

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

[Ram]

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

[Inquisitive8995]

Thank you. I was not aware of that previously.

Answer 1

[h.mon]

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.

[Inquisitive8995]

Thanks I will try this.