Measuring expression of repetitive elements?

[Alex234]

Hello, I would simply like to asses the expression levels of all types of repetitive elements in my RNA-Seq samples.

I assume that these are not being aligned in the first place by TopHat2?

Could someone tell me a way of doing this?

Thanks!

Alex

[vas72985]

Several studies have attempted to do this and unfortunately none of them have done it in a manner that actually looks at authentic repetitive element transcripts. The problem arises from the high prevalence of repeats in the primary transcripts of cellular mRNAs (nearly all cellular mRNAs have some kind of repeat in their introns or UTRs). Simply mapping RNAseq data to repeat element consensus sequences ignores this facet of repetitive element biology, so rather than looking at authentic repetitive element expression, all of the papers that have been published on this subject are likely just measuring the presence of repetitive element sequence in the mRNAs of other genes.

[Alex234]

Hi vas72985,

I have tried to get around this problem by only counting uniquely mapping
reads (with no mismatches) that map to intergenic repetitive elements,
although this probably is excluding the majority of genuine repetitive element
expression, so I am not sure how valid it is.

Still I find some expression differences, but am not sure whether these are representative of the element type in question, having thrown out the majority of non-uniquely mapping reads. Presumably, only the expression of individual repetitive elements can be 'validated' by qPCR (by exploiting unique mutations in their sequence)?

Would be interested to know what you think,

Thanks,

Alex

[Gonza]

Hi All,

I will be soon mapping repetitive sequence and I have a couple of questions. It is my understanding that it is error-prone to map repetitive sequences. Is this something that tophat2 can take care of by simply tweaking the parameters? for example, I could set the -N/--read-mismatches to 0. Or is there something more 'fancy' that needs to be done?
Also, is it worth it to pay more and do paired-end sequencing to be more accurate in mapping to repetitive regions?
Thanks.



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