SortMeRNA for multiple reads file

Question

[uvika85]

Hi,

I wanted to run SortMeRNA for multiple reads file. but as I know SortMeRNA handles only single file at once. Although it is working on a single fastq file, I wanted to run it on my whole folder which consists of 59 fastq file. I don't know anything about bash. can anybody help me?

sortmerna \
  --ref ./rRNA_databases/silva-bac-16s-id90.fasta,./index/silva-bac-16s-db:./rRNA_databases/silva-bac-23s-id98.fasta,./index/silva-bac-23s-db:./rRNA_databases/silva-arc-16s-id95.fasta,./index/silva-arc-16s-db:./rRNA_databases/silva-arc-23s-id98.fasta,./index/silva-arc-23s-db:./rRNA_databases/silva-euk-18s-id95.fasta,./index/silva-euk-18s-db:./rRNA_databases/silva-euk-28s-id98.fasta,./index/silva-euk-28s:./rRNA_databases/rfam-5s-database-id98.fasta,./index/rfam-5s-db:./rRNA_databases/rfam-5.8s-database-id98.fasta,./index/rfam-5.8s-db \
  --reads SRRXXXXXXX.fastq --aligned SRRXXXXXXX_rrna \
  --other SRRXXXXXXX_sortmerna --fastx --log -a 4

[h.mon]

Questions about bash loops have been asked many times before, please search the site and try the suggestions proposed at some of them. Some examples:

HISAT2 for loop shell scripting

Even questions about SortMeRNA loops have appeared before:

Running SortMeRNA for bulk RNAseq data

Run merge-paired-reads script for multiple files at the same time (SortMeRNA)

[uvika85]

well, I know similar question being answered many time. I wanted to know that if I can process it without bash scripting. because don't know anything about bash Thanks

[h.mon]

When you run SortMeRNA on the command-line, you are already "bash scripting" - you already know more than you think you know.

You can use GNU parallel or snakemake to process several files without (sensu strictu) bash scripting. But, in my opinion, they are more difficult than plain bash scripting, although a lot more powerful.

[Carambakaracho]

You can - provided you can use some advanced excel. Put each variable list (file names etc) in one column each, your formula in the last. Replace filenames with pointers to adjacent cells to create strings with your command, copy to all cells below.

very limited, but works for your use case.

[uvika85]

ok. thank you soo much . I will try that.

[uvika85]

Hi, I am very hopeful that you will sort my problem. I am having multiple files for analysis. I am running sortMeRNA with the command below.

sortmerna --ref ./rRNA_databases/silva-arc-23s-id98.fasta,./index/silva-arc-23s-id98.db:./rRNA_databases/silva-bac-23s-id98.fasta,./index/silva-bac-23s-id98.db:./rRNA_databases/silva-euk-18s-id95.fasta,./index/silva-euk-18s-id95.db:./rRNA_databases/silva-euk-28s-id98.fasta,./index/silva-euk-28s-id98.db:./rRNA_databases/rfam-5s-database-id98.fasta,./index/rfam-5s-database-id98.db:./rRNA_databases/rfam-5.8s-database-id98.fasta,./index/rfam-5.8s.db --reads path_to_file/*.fastq --aligned rrna --other sortmerna --fastx --log -a 4

How can I change the output file name, filename.fastq from above, to reflect the name of the initial input files?