I am new to RNA-Seq. I am working on a RNA-seq data set from the mouse genome. I have ran some quality testing using the fastqc and fastx software. I have found out that the data set is full of rRNA reads.
I would like to filter there reads out, but I am not sure how to go forward with this. I have also read this post, but it didn't help much.
As I have done the mapping against the ensembl GRCM38 version, I guess it is better to work with the ensembl file. But how to do the filtering?
Is there a way to filter the rRNA reads before the mapping?
I know I can convert the gtf files into GenomicRanges object. BUT will that help me to remove the reads mapped to this coordinates after the mapping. if so how?
The last option, as reads in the above mentioned post is to take the list of rRNA ensembl IDs and just filter the list of results from featureCounts or HTseq-count to remove those rRNAs from it.
Is this option better than the other two?
thanks in advance for any information