SquiggleKit Using RNA for MotifSeq

Would there be a possibility to simulate RNA squiggles and perform motif search ?

Mar 24 '20 14:03 epi-gene

Hello,

yes, just use the following flag --scrappie_model squiggle_r94_rna

Mar 24 '20 23:03 Psy-Fer

Hi. I tried the above but the motifseq is yielding no results. The hit probabilities are 0 for all the reads.

Mar 25 '20 15:03 epi-gene

Is there a way to calculate them manually ?

Mar 25 '20 15:03 epi-gene

Could you please give me an example of the output? I'll look into it. I have some RNA data on hand to double check.

Mar 26 '20 01:03 Psy-Fer

fast5 | readID | model | start | end | length | distance_score | model_mean | model_stdev | Z-score | p-value | hit_Probability 8e91fa7d-fd33-422b-8dfb-69915b17aa8d.fast5 | 8e91fa7d-fd33-422b-8dfb-69915b17aa8d | last50 | 11839 | 12071 | 232 | 399.438241083274 | 135.4 | 11.465672 | 23.0285883883015 | 1 | 0

Mar 26 '20 07:03 epi-gene

You did mention

The p-values and hit probabilities provided are based on loose modelling of negative background scores for a number of k-mers. It is currently only modelled on R9.4 model, not R10 or RNA in the readme.

Mar 26 '20 07:03 epi-gene

@Psy-Fer Would MotifSeq be able to detect multiple Motif hits within a single read ? Or would it display only the high scoring hit ?

Apr 29 '20 15:04 epi-gene

Currently, only the highest scoring hit.

I plan on allowing it to record more than the the top hit.

A round about way of "hacking" a solution, is to just mask out the region of the best hit, and try again. So, just take the values between the start and stop site, and change them to the mean current, or make them 99999 and they will get filtered out altogether. Obviously that isn't idea, and i'll try fixing this.

Apr 30 '20 05:04 Psy-Fer

Ok. Will try that.

Apr 30 '20 07:04 epi-gene