User: ben.kunfang

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ben.kunfang10
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Posts by ben.kunfang

<prev • 10 results • page 1 of 1 • next >
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Comment: C: New ultraperformant version of SICER/epic: epic2
... Hi, endrebak I was wondering if epic2 is specific for dispersed histone mark or there is any way to call sharp mark peak with epic2? Thanks! Kun ...
written 9 days ago by ben.kunfang10
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Different parameters for macs2 to call narrow marks and broad marks?
... Hi, I was wondering how to set different parameters for macs2 to call different histone marks? I have seven marks: H3K4me1, H3K4me3, H3K27ac, H3K36me3, H3K79me2 H3K27me3 and H3K9me3. In my knowledge, H3K4me3 and H3K27ac should be narrow peak, H3K36me3, H3K27me3 and H3K9me3 should be broad peak. H3K ...
peak histone modification macs2 chip-seq written 9 days ago by ben.kunfang10
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Comment: C: Ideas to split peaks into subpeaks - beyond PeakSplitter
... Hi, Rashedul I was wondering if you can give the link of FindER's paper? I just can't find it, thanks! Kun ...
written 9 days ago by ben.kunfang10
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Comment: C: Why the estimated fragment length result is different between SPP and macs2 pred
... Good idea~but I think the estimated fragment length indeed affects the position of the peak. I used two fragment lengths separately to call the peak(macs2) and intersect the narrowPeak file. 88627/112435 are overlapped, which mean 25% of peaks are in different regions. In this case, I might not say ...
written 19 days ago by ben.kunfang10
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how to deal with H3K4me3 and H3K4me1 overlap peaks?
... Hi, I downloaded MCF7 H3K4me1 (ENCFF191EBN) and H3K4me3( ENCFF132IPF) narrow peak file from ENCODE website and I found a portion of peaks are overlap with each other. But in real world, H3K4 cannot be monomethylated and trimethylated at same time. So I was wondering how to deal with those peaks? I ...
peak histone modification macs2 chip-seq written 20 days ago by ben.kunfang10
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Comment: C: Why the estimated fragment length result is different between SPP and macs2 pred
... Thanks for your reply! I tried csaw, and it indeed has two local peak one around 140 one around 280. Two algorithms might have different thresholds to select the local peak. ...
written 20 days ago by ben.kunfang10
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Why the estimated fragment length result is different between SPP and macs2 predictd?
... Hi, The data I use is ENCFF424GON. When I use ENCODE ChIP-seq pipeline on DNAnexus and use SPP(xcorr) to calculate the estimated fragment length, it gives me 140bp, however, when I use macs2 predictd function with parameter -g hs -m 5 50, it gives me 274bp. I try several mfold combinations but no o ...
macs2 spp estimate fragment length written 21 days ago by ben.kunfang10
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How to get the pooled-replicate narrowPeak file for IDR peak-list
... Hi, I am newbie for peak calling. When I am trying to follow ENCODE's pipeline to merge narrowPeak from replicates, I stuck with this pooled-replicate narrowPeak file to run IDR. I check the IDR github and it says "Run idr using an oracle peak list (e.g. peaks called from merged replicates)", which ...
pooled-replicate idr written 27 days ago by ben.kunfang10
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(Closed) why nucleosome spacing is longer in heterochromatin than euchromatin
... Heterochromatin is defined as tightly packed form of DNA. But some experiments show that the average spacing of nucleosomes associated with H3K9me3 and H3K27me3, both heterochromatin marks, are longer than those with euchromatin marks. why packed DNA has longer spacing? ...
heterochromatin nucleosome spacing written 4 months ago by ben.kunfang10
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Answer: A: understanding bamtobed output
... I think its represent to MAPQ score, see detail in this thread:https://www.biostars.org/p/150954/ ...
written 16 months ago by ben.kunfang10

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