Skip to main content
1 vote
Accepted

Statistical methods suitable for DE analysis of non coding RNAs

There is no question that lncDIFF is the approach to use, especially if the alternative is performing edgeR directly, and thats demonstrable (below). I don't think anyone would question the legitimacy ...
M__'s user avatar
  • 12.8k
1 vote

Target genes for piRNA

Update It does indeed appear that while piRBase etc. have human piRNAs, they do not have target information. Looking at related questions, recommendations are made to map piRNA sequences to the genome ...
Maximilian Press's user avatar
1 vote
Accepted

Is is possible to predict ncRNAs from sequence and homology alone?

Is there any conserved secondary structure in this RNA? One could align all known instances of this RNA and see if there is any significant covariation according to R-scape. That could serve as a ...
apetrov's user avatar
  • 26
1 vote

Are there databases to annotate non-coding mutations?

VarSome allows you to annotate any variant, including non coding ones. While ACMG classification will not be available if the variant isn't in a gene's transcript (the ACMG criteria are only ...
terdon's user avatar
  • 10.4k
1 vote
Accepted

Which tools are available to call somatic mutations on non-coding regions from whole genome sequencing data?

Those will have to be treated as separate analysis. You can use Mutect or VarScan for the matched samples and the tools listed in the other question for the unmatched samples however that means that ...
Bioathlete's user avatar
  • 2,584

Only top scored, non community-wiki answers of a minimum length are eligible