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This is a proposal for a new term "Manual motif instance prediction based on multiple sequence alignment" as used in the CollecTF database (www.collectf.org). Manual motif instance prediction based on…
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Hi Taoliu,
I am using macs2 for CUT&RUN transcription factor peaks. My biologist colleagues pointed out some peaks that are not called, but are visible in the rpm-normalized bedgraph visualization,…
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`runParca.py --debug-parca` raises `KeyError: 'FNR-4FE-4S-CPLX__FNR-4FE-4S-CPLX__active'`.
This might depend on which transcription factor condition it randomly selects.
It's also possible that …
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Hello Laurence, I am working with Claire Lehenaff on prophages, bacterial diversity and interactions in beverages fermentation context. We would try to investigate social genes in one of our specific …
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I read the CENTIPEDE manuscript. I think the author scanned all putative TFBS across the genome.
However, in your tutorial, you suggested using FIMO only to obtain TFBS in peak regions.
Is it pr…
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Hi,
Is there a specific option to set when run macs2 in broad mode in order to get summit location? I want to call broad peaks for histone modification, when I run the following command:
```
ma…
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see GO ticket go-ontology/issues/23135
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Hi,
I have been able to succesfully run the RGT-Hint pipeline according to the tutorial on the website (https://www.regulatory-genomics.org/hint/tutorial/) to conduct footprinting and differential …
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Currently the definition of gene http://purl.obolibrary.org/obo/SO_0000704 is _A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may …