-
Hi all,
Thanks for this great tool! I have a question on its use though.
Could the user examine the binding specificity of the motifs in your models by querying a sequence > 10000b introducing an …
-
## LoL
1. On which protein is the first ChIP-Seq is performed?
1. In ChIP-Seq, what factors contribute to a spurious peak? What experimental/computational procedures can you take to reduce such no…
-
Hi,
Reading of models built from DNA sequences appears to fail: below I show an example using a motif from the Dfam database ([DF0000029](http://dfam.org/entry/DF0000029)).
```
cp = hmm.HMM.cre…
-
Hi, After I make the cluster by the Clustering/fit function, is there anyway or convenience way to predict a new incoming TCR peptide sequence and assign a (existing) cluster number to it. I know I c…
-
Hi,
I am trying to determine the insertion target site of my LTR/Gypsy elements. Using **10:22687853..22691116_INT** as an example, I assume that:
scaffold name = 10
start_position = 22687853
…
-
I see a lot of cases when a TF has motifs falling into distinct clusters. Is there a preferred strategy to select the likely correct WT motif for each TF and allocate each TF to one motif cluster?
…
vitkl updated
2 years ago
-
Hi I was testing your tool on a sample and wanted to check the copy number in a specific region.
if I understood correctly the MC tag in the info field corresponds to the copy number of the motif in…
-
Is there any documentation to explain in details how to write complex queries with motif finding DSL?
I want to write a DSL that shows if a node is connected to another node at any n-level but don…
-
Hi,
As the title states, I'm unfortunately unable to calculate P value for several large motifs, the most important for me being CTCF motifs. I tried using several different motif databases, includ…
-
**Is your feature request related to a problem? Please describe.**
I'm guessing most people would rather work with a PWM as a numpy array. Numpy is already a dependency for gimmemotifs, so it wouldn'…