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I would like to do a genome-wide search for enriched motifs after performing the footprinting on ATAC-Seq data. I am aware that there is a tool called HOMER to do that. However, HOMER only accepts a b…
czfoo updated
4 years ago
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Hello,
I'm new to scATAC analysis. I watched your presentation in the recent Illumina event and would like to use signac in our analysis. You mentioned that signac does a better job in calling peaks.…
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Hi @lpantano,
I have seen that you are adding support for deeptools bamcoverage, thanks a lot for this, really nice. I was just wondering if these two parameter
--extendReads 150 --centerReads cou…
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Check. Silencing is the default for centromere, some of these seem to be "increase in the extent of chromatin silencing"
increased chromatin silencing at centromere
- [ ] cut8 (1-72) (73-262 Δaa)…
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Hi snakePipes, thank you for the great pipelines. I would like to ask if it is possible to add 'single strand' option to the ATAC-seq pipeline?
Inspiration:
https://github.com/taoliu/MACS/issues/…
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Hi all,
The sequencing depth of single cells would be an important factor that may hinder true discovers like cell type identification, pseudo-time paths calculation etc. As far as I know, man…
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All of the GO "chromatin silencing' terms will be merged into correspondeing "heterochromatin assembly" terms.
Therefore, andy logical desf which use them will need to be defined differnetly (…
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I hadn't seen
heterochromatin domain assembly before
The aggregation, arrangement and bonding together of a set of components to form a heterochromatin domain.
how does this differ from the parent…
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Hi Colin
https://pubmed.ncbi.nlm.nih.gov/18270511/ confirms RBP2 (KDM5A, P29375) binds a 6 base motif CCGCCC, has enzyme activity and regulates transcription. In November I annotated this as a dbTF…