What is index in sortmerna?

Question

[taufiqbge]

Hi, I am a beginner of NGS data analysis. I am using SortMeRNA to remove rRNA from my mapping sequence. I read all the available instruction SortMeRNA but still confused. My command is-

 ./indexdb_rna --ref ./silva-bac-16s-id90.fasta, ./folder containing input fasta file --reads ./folder containing input fasta file/input.fastq

ERROR: -m [INT] must be a positive integer value (in Mbyte).

Any help would be much appreciate.

[GenoMax]

Multiple things you need to pay attention to.

You can't use random , in your command lines. ./folder containing input fasta file need to be replaced with a real entry` (did you copy that from the manual example command line).

./indexdb_rna --ref ./rRNA_databases/silva-bac-16s-id90.fasta,./index/silva-bac-16s-db -v

[taufiqbge]

Thanks for your reply. I checked the (,) and also went through the manual. I just mentioned "folder containing input fasta file" to ensure that the path is correct before and after the --reads. However, still I am getting error. I input fastq file which is already mapped.

[GenoMax]

Ah I see. You used folder containing input fasta file as an indicator that you have a real value there.

I posted an example command for the indexing step from sortmerna manual. This is done independently of running sortmerna. You don't provide any reads/alignments in this step.

After the indexing is complete you provide aligned reads when running the program.

./sortmerna --ref db.fasta,db.idx --reads file.fq --aligned base_name_output

[taufiqbge]

Sorry for not understanding the trick. Just confused that should I make a folder name "index" in the same path. I am confused this portion only-

> *./index/silva-bac-16s-db -v*

Thank you for your assistance.