rRNA contamination in RNASeq fdata

Question

[rajdeepboral00]

Hello all, I want to see whether my RNASeq data contains rRNA contamination, which tool would be most efficient forthat? I have tried using sortmerna but due to whatsoever reason i am unable to build index file using indexdb_rna command (this is not getting downloaded) if there is any other tool then please suggest.

Answer 1

[dsull]

You could just download rRNA sequences (in FASTA format), index them with bowtie2, and align your reads to them, and see how many reads aligned.

There are many previous Biostars on where to download rRNA sequences in FASTA format, e.g. downloading human rRNA.fasta