Dear all,

I am working on an organism that has 10 copies of rRNA genes on its genome. I would like to see the percentage of reads that are aligned to ribosomal RNA.

After alignment, rRNA reads align to every and each of these genes and if I perform the counting for reads that are not uniquely aligned to the genome, each one of these reads are counted 10 times. How can I count each read only once?

Any idea is highly appreciated.

Thanks
Hi, I am not sure whether this is the option that works best for you. But, I suppose you can get what you want using [Tagdust2][1]. Basically you provide the sequences of rRNA genes (I usually generate this using [BioMart][2]). I have used this in the past to remove rRNA reads before genome alignment. Run Tagdust2 and then take a look at the TagDust2 output summary file. If you do this following math you will get the number you want.

rRNA reads = total input reads - successfully extracted

When you do this, these rRNA reads will be saved on to a separate .fq file which you can use for any other downstream analyses you want to perform. May be an advantage for you.

To run Tagdust2:

> tagdust -t 8 -1 R:N -o /path/to/output/ -ref /path/to/rRNA.txt -fe 2 /path/to/input.fastq

I hope this will help! 


  [1]: http://tagdust.sourceforge.net/
  [2]: https://m.ensembl.org/biomart/martview/8ede409a16af70d56987a76ec8ba2422