CDieterich comments

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                                            CDieterich

reads did not aligned to 3' end

Same problem over here for direct RNA-seq. Running NanoSim3.0.2 EEF1A1 is on the minus strand.. I would expect a 3'end read bias, but see an increased coverage at the 5'end.

reads did not aligned to 3' end

Top 2 tracks are from NanoSim

RNA model for bonito

Excellent.

RNA model for bonito

BTW, is there any manual to do the training myself ?

RNA model for bonito

Ok, got back to this now.. any developments on this aspect (RNA modifications) @iiSeymour ? I would be happy to do it myself provided that there is some documentation for...

Module to design siRNAs

https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw1325

Module to design siRNAs

I would like to push this to Version 0.3.0 Do you agree ?

duplicate reads in the count matrix with difference expression value?

Hi @gnilihzeux and @mathavanpu what kind of sequencing library do you use and does the backsplicing junction fall into a known exons ?

Check correctness of stranded work flow

Well, antisense transcription exists, but should be rare. We can look at it together next week > Am 30.09.2016 um 18:08 schrieb Tobias Jakobi [email protected]: > > Current runs show...

Check correctness of stranded work flow

Hi Tobias, I have run the polysome sequencing date from the eLife Doudna paper (PMID: 26735365), which is unstranded. Same problem on hg38 2 20254863 20256170 PUM2 1 - exon-exon...