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Hi,
So far I have been using the default database that comes bundled with Gimmemotifs, which is quite alright for most purposes. However, Jaspar 2018 has just been released and I wanted to repeat s…
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Currently, search has a button for "Custom" but it does not clarify what type of custom files it accepts.
Since search allows for custom motifs and for custom structures to be included it would ma…
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Hi, thanks for developing this great tool! I have a question about how the motifs are identified. In the example below, I am wondering why longer motifs, such as `TCCCCTCCCACCCGG` are not identified. …
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Hi,
I ran trgt on version 1.0 trgt annotation https://github.com/PacificBiosciences/trgt/issues/37#issuecomment-2274126461_ and one of the complex TR:
> chr19 53958673 53959528 ID=…
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For some datasets, oligo-analysis returns highly significant k-mers, but
- the assembled matrix is of poor complexity (basically, the matrix contains a succession of Gs)
- `position-analysis` retur…
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Can we add the primers for SSR and RFLP markers to the records in GlycineMine? Example Satt430 does not present the primer sequences just the motif. This might also be a datastore issue? @adf-ncgr @S…
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Dear basenji developers,
I would like to use basenji to model ChIP-seq data. In particular I would like to train a model using the ChIP-seq data for a certain transcription factor (TF). The data can …
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Dear author,
I am running the REforge but it is too slow. I have 226,746 CNEs and downloaded the 879 motif matrix of vertebrata from JASPAR. I chose to run by submitting the task in slurm. I split …
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Thank you so much for your excellent work on this method!
I was wondering if there is currently a way to specify that I would like the generated scaffold to occupy its own chain. For example, if I …