Can we use Ribodetector for rRNA quantification in scRNASeq?

[Rohit-Satyam]

I have UMI based (3' chemistry) scRNAseq. The R1 file therefore contains 28bp long UMI+barcodes and R2 file contains the actual reads. Since Ribodetector objects anything below 30bp and warns user that the prediction of rRNA reads might not be accurate, I was feeling reluctant to use both R1 and R fastq files. But if I run it just on R2, how will I be albe to subset R1?

Do you plan to add support for scRNAseq data in future?

[dawnmy]

Thank you for your suggestion regarding scRNA support. I will consider its inclusion in future updates.

For now, you can run it on R2. After this, you can retrieve the read ID of the predicted rRNA reads using:

seqkit seq -ni <your rRNA fastq from R2>  -o id.txt

This will generate an id.txt file. Once you have this list of read IDs, you can then fetch the corresponding records from your R1 fastq file using:

seqkit grep -f id.txt <R1 fastq file> -o <filtered R1>

Of course you need to install seqkit with conda first.

I hope this helps, and please keep us posted with any further queries or feedback!