Quatification of tRNA-derived RNA fragments (tRFs) ?

[diego diaz]

Hi,

In the lab we are analyzing tRNA-derived RNA fragments. My boss needs to quantify these fragments in different conditions (Presymptomatic ALS and Symptomatic ALS) to check if there are some fragments differentially expressed.

The model is Mus musculus (mm10).

The main problem is that most of the tRNA genes are redundants. Therefore, when the reads that were generated from these genes are mapped, the program (bowtie) assigns them randomly, or reports all the sites (depending on the configuration), causing bias in the cuatification.

Is there a less biased way for quantifying tRNA-derived RNA fragments?


Thanks in advance!!

[RNA_]

Hi Diego,

I'm having the same problem now, but need to quantify tRNA fragments for a different purpose. I was thinking of making a tRNA "genome" based on the consensus sequences of each tRNA isoacceptor so that each tRNA is only present once. My goal is that tRNA reads would only have one place to map to. I don't think it's ideal but it's the best I have so far.

Have you, or has anyone else, resolved this?

[GenoMax]

@RNA: Not sure if it would directly help but take a look at this paper: http://www.nature.com/articles/srep07675#methods

[RNA_]

Thanks for the quick reply GenoMax. That's definitely helpful.

[RNA_]

For anyone else interested:

tDRMapper: http://bmcbioinformatics.biomedcentr...859-015-0800-0