Closed igordot closed 9 years ago
Given a position weight matrix for a transcription factor, the list of motif instances is typically generated by scanning the genome for sequences that have a higher likelihood under the PWM model than a background model. Since the format for PWM matrices tend to vary and users might want to only include a subset of all motif instances, we decided to let this be an input generated by the user separately. Thanks for the suggestion; I will update the documentation with this description.
I know there is at least one database (http://compbio.mit.edu/encode-motifs/), but it's human only. Any additional resources or tools would be very helpful.
Sorry. Do you have any updates on this topic?
The encode database is quite useful. Another database of PWM models for human and mouse factors is from this paper. http://www.sciencedirect.com/science/article/pii/S0092867412014961
Two other commonly used databases of PWM models are TRANSFAC (http://www.gene-regulation.com/pub/databases.html) and JASPAR (http://jaspardev.genereg.net/), which have models for factors in other eukaryotes.
Hope this helps!
This is not really an issue (maybe a documentation issue). The tool takes two inputs. One is a BAM file, which makes sense. The other is a file of motif instances. Do you have any suggestions on where to get or how to generate that file?