RNA004 Inverted DRACH Results

[BrendanBeahan]

My team recently ran xPore on both an RNA002 and RNA004 dataset. The RNA004 dataset, understandably, resulted in some pretty strange outcomes. In particular, the RNA004 output seemed to have an inverse relationship between the statistical significance of the predicted modification and the amount of DRACH enrichment said site was associated with. This is the opposite of what we observed in RNA002.

I suppose I'm just curious if your team had any insights into how you underlying method may lead to such an outcome or if this seems like a plausible outcome?

[yuukiiwa]

Hi @BrendanBeahan,

The main branch of xpore hasn't been updated to support RNA004. You can provide the RNA004 kmer model (https://github.com/GoekeLab/xpore/blob/RNA004_kmer_model/xpore/diffmod/RNA004_5mer_model.txt) during in the xpore diffmod config.yml when running xpore diffmod:

data:
    <CONDITION_NAME_1>:
        <REP1>: <DIR_PATH_TO_DATA_JSON>
        ...

    <CONDITION_NAME_2>:
        <REP1>: <DIR_PATH_TO_DATA_JSON>
        ...

    ...

model_kmer: <PATH_TO_KMER_MODEL>

out: <DIR_PATH_FOR_OUTPUTS>

Thanks!

Best wishes,
Yuk Kei

[NStrowbridge]

Hi, @yuukiiwa

To jump on this, is it possible to compare between RNA002 and RNA004 data. I have data from multiple replicates of both. I.e. 4 samples per condition, 3 conditions, with 2 samples sequenced with RNA004 and 2 with RNA002. I was originally using m6anet to call data separately and then trying to perform differential methylation with that output, however, it seems that xpore might be a better idea.