User: Jingyue
Jingyue • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- United States
- Last seen:
- 1 week ago
- Joined:
- 4 years, 7 months ago
- Email:
- j***********@uconn.edu
Posts by Jingyue
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Comment:
C: ATAC-seq 150bp reads
... Hi, ATpoint,
Thanks for the insightful answer!
I plan to send out my sample for sequencing. Do you think sequencing ATAC library at a short length directly would be better? Like 35bp paired end reads. Or do long reads 150bp and then clip it shorter by some tools?
Thank you! ...
written 9 days ago by
Jingyue • 30
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... Hello,
Do you also merge the differential binding regions among these different tools?
Thanks! ...
written 4 months ago by
Jingyue • 30
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... Hello all,
Do you recommend to overlap two or more differential peak calling tools to get a more stringent/accurate differential peaks?
Thank you! ...
written 4 months ago by
Jingyue • 30
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... Hi, Rory,
Thanks for the software, I'm wondering do you recommended overlap the differential peaks between softerware, like between DiffBind and Csaw? Will this give a better/accurate differential results? ...
written 4 months ago by
Jingyue • 30
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... You can use Csaw (https://bioconductor.org/packages/release/bioc/vignettes/csaw/inst/doc/csaw.html) it use window-based method for differential binding analysis and can avoid using peaks from MACS2. ...
written 6 months ago by
Jingyue • 30
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... Hi,
Do you think average plot over "peak count frequency" compare to other method like deeptools plot over "normalized read depth", which one is more informative?
Thank you! ...
written 6 months ago by
Jingyue • 30
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... I would like to plot the ChIP peaks binding enrichment around its binding center.
I plotted this using deeptools, but would like to see how it look like in ChIP-seeker.
ChIP-seq inputs are peak.bed files, so I don't think is over bam/bigwig files
Thank you! ...
written 6 months ago by
Jingyue • 30
0
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255
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... Hi,
I'm wondering how to plot the heatmap around the peak center in ChIPseeker? Can I plot 3 samples in 1 plot? Do I need a merged peak file?
Here is the code I use to plot around TSS, but don't know how to do it for peak center.
Thank you!
promoter <- getPromoters(TxDb=txdb, upstre ...
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Comment:
C: Using Diffbind R-studio
... Hi, Devon,
I would like to know if you overlap Csaw DB regions back to MACS2 peaks in the downstream? Thank you! ...
written 6 months ago by
Jingyue • 30
0
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... Dear all,
I have a question of downstream analysis after I got the differential binding (DB) region from Csaw tool, which used a window-based method.
My questions are:
- Since it is not a peak involved method, do I overlap these DB region (window-clustered region) back to my MACS2 p ...
written 6 months ago by
Jingyue • 30
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