User: Jingyue

gravatar for Jingyue
Jingyue30
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

<prev • 25 results • page 1 of 3 • next >
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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 Jingyue30
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Comment: C: Differential Peaks Between Replicates
... Hello, Do you also merge the differential binding regions among these different tools? Thanks! ...
written 4 months ago by Jingyue30
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ChIP-seq differential binding analysis tools
... Hello all, Do you recommend to overlap two or more differential peak calling tools to get a more stringent/accurate differential peaks? Thank you! ...
csaw diffbind chip-seq written 4 months ago by Jingyue30
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Comment: C: What is the best method ChIPseq differential binding analysis?
... 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 Jingyue30
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Answer: A: Performing differential binding analyses between ChIP samples using Deeptools (S
... 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 Jingyue30
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Comment: C: 2 peak files in plotAvgProf2 [ChIPseeker]
... 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 Jingyue30
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Comment: C: Chip-seeker heatmap around the peak centers
... 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 Jingyue30
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Chip-seeker heatmap around the peak centers
... 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 ...
R chipseeker written 6 months ago by Jingyue30 • updated 5 months ago by zx87549.0k
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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 Jingyue30
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Downstream of Csaw differential binding region
... 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 ...
csaw peaks chip-seq differential binding written 6 months ago by Jingyue30

Latest awards to Jingyue

Supporter 6 months ago, voted at least 25 times.
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Running Cuffmerge error "duplicate/invalid 'transcript' "
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Running Cuffmerge error "duplicate/invalid 'transcript' "
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Running Cuffmerge error "duplicate/invalid 'transcript' "
Popular Question 3.6 years ago, created a question with more than 1,000 views. For Running Cuffmerge error "duplicate/invalid 'transcript' "

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