User: gable_works

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gable_works20
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Posts by gable_works

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Answer: A: How can I find motifs under individual ATAC-peaks?
... I've had success with [RGT-HINT][1] which provides a motif enrichment tool. In addition the .bed file produced can be dropped into a genome browser with labeled 'motif matches'. That way you can visualized these matches at your peak of interest. [1]: https://www.regulatory-genomics.org/motif-ana ...
written 17 days ago by gable_works20
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Comment: C: Paired end peak callers
... The duplicate data is consistent with both peak callers. I agree that the complexities of ATAC data can be independent of TFs and that some TFs may provide open chromatin states while others may not. ATAC and ChIP data would be interesting to analyze alongside depletion conditions. I think moving fo ...
written 18 days ago by gable_works20
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Comment: C: Paired end peak callers
... 1) I have ATAC in duplicate from multiple cell lines. 2) We find MAC2 called more peaks than Genrich and these peaks were validated with ChIP-seq data of TFs. Consistently MAC2 yielded 100K peaks and Genrich 50K (per50mil reads, although peaks platuea [genome biology][1]). [1]: https://genome ...
written 21 days ago by gable_works20
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Comment: C: Paired end peak callers
... They certainly on average tend to overlap with MACS2 peak caller. But we found sites where Genrich did not call peaks when we clearly have ChIP-seq data of TFs overlapping. As seen in the image, the middle shows that Genrich did not call a peak where MACS2 did, and there is evidence of a TF bound at ...
written 22 days ago by gable_works20
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Comment: C: shift direction in ATAC/DNase data?
... `--nomodel --shift 100 --extsize 200` is intended to assess Tn5 cut sites and represents cut site enriched fragments for peak calling analysis. Some of these [parameters][1] have been discussed. `--nomodel` does not exclude shifting it just doesn't build a shifting model. [MACS2][2] documentation st ...
written 26 days ago by gable_works20
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Comment: C: Paired end peak callers
... Although our downstream differential transcription factor (TF) analysis results remained similar between both peak callers we found that MACS2 called more peaks and we validated these peaks from ChIPseq data of TFs. We reasoned that if an ATAC-seq peak overlaps a ChIP-seq TF peak then the peak calle ...
written 26 days ago by gable_works20
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Answer: C: Paired end peak callers
... Both [Genrich][1] and [MACS2][2] can call peaks on paired-end ATAC-seq data and remove duplicates. Multi-mapped reads are typically removed/disregarded during the alignment step (i.e. [bowtie2][3]). Removing mitochondrial reads can be accomplished with [multiple methods][4] of which I prefer using ` ...
written 26 days ago by gable_works20

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