NeoLoopFinder

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Neoloopfinder doesn't find loops and assemblies that I think it should

1

H Xiaotao, great tool filling an urgent unmet need. I am running neoloopfinder on the following SVs: ``` chr1 chr1 ++ 198179654 205207358 translocation chr1 chr1 -- 198993881 198984836 translocation...

auberginekenobi

Could you give me some guidelines to manually review and validate the neoloops and neotads

1

Xiaotao, I am using neoloop to produce some neo-loops and neo-tads (some rows with the last columns as "1"). But I am interested in validate whether they are really neo-loops/...

wzhang42

Some questions for positive and negative training dataset

1

Xiaotao, 1.) In your NC peakachu paper, Fig.1 mentioned GM12878 is used for the training dataset. But in the Supplementary Data 1, GM12878, K562, H1ESC, and mESC are used for...

wzhang42

How to output the Regular loop and Tads without SVs

4

Hi, Xiaotao. I am now using NeoloopFinder to detect Neoloops/Neotads. But I found one Neoloop was not reported (even the last column tag as 0) from NeoloopFinder. I traced back...

wzhang42

How do I handle cool files

1

Hello, there are some problems when I use it, there should be some problems with my cool file, I used Juicer to generate Hic file and then converted it into...

shidetong

calculate-cnv runtime error

4

Hi there and thank you for this great tool. I'm trying to run CNV-normalization on MNase-digested HiChIP samples that had been processed through HiC-Pro and JuicerTools to make hic maps....

katreya42

assemble-complexSVs "Called 0 connected assemblies"

1

I have no idea why I got all zero in assemble-complexSVs.... Inside my breaks.sv.txt file would be like this.. chr15 chr2 -+ 35700000 216100000 translocation chr1 chr15 +- 109750000 101140000...

DittmanC

CNV adjustment

3

I have adjusted the CNV using calculate-cnv, segment-cnv, and correct-cnv. After that, I was trying to see in the triangular plot of the cool file at the same region. Basically,...

DittmanC

compatibility with hiChIP data

3

Hi this is more of a question than an issue. I was wondering if NeoLoopFinder can be applied to H3K27ac HiChIP, given the enhancer hijack use case as illustrated in...

SplitInf

I ran assemble-complexSVs. The SVs are deletions and duplications. I got no output. The assembleSVs.log file has the fowllowing content: root INFO @ 08/17/21 19:23:57: # ARGUMENT LIST: # Output...

zhangli271828