User: Ben

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Ben50
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Posts by Ben

<prev • 49 results • page 1 of 5 • next >
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Directionality Index analysis from Hi-C
... Does anyone know how to calculate Directionality Index from Hi-C data? Thanks in advance! ...
directionality index written 21 months ago by Ben50
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Answer: A: cuffdiff long noncoding annotation vs full annotation
... You should align the clean reads to reference genome with the lncRNA gtf, then you can run cuffdiff using the lncRNA gtf ...
written 2.5 years ago by Ben50
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Answer: A: Prediction of lncRNA cis regulation
... you can see my paper titled "Functional prediction of differentially expressed lncRNAs in HSV-1 infected human foreskin fibroblasts" ...
written 2.7 years ago by Ben50
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Comment: C: THOR a HMM based approach for differential peak calling with replicates
... Could you explain the THOR in detail? ...
written 2.8 years ago by Ben50
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Comment: C: how to calculate p value
... I need to calculate the difference of two ChIP-seq, not one ChIP-seq and input ...
written 2.8 years ago by Ben50
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how to calculate p value
... I have two ChIP-seq data, including Case and Control sample. The reads in ChIP-seq followed Poisson distribution, so how to calculate the difference and p value in peaks identified in ChIP-seq. ...
R chip-seq rna-seq written 2.8 years ago by Ben50
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extract the number of reads around TSS
... I have coded oen python script to extract the amount of reads around TSS from ChIP-seq sam file, but the speed is too slow. Does anyone have any suggestions to solve this question? Thanks in advance! ...
chip-seq written 2.9 years ago by Ben50 • updated 2.9 years ago by Alex Reynolds30k
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Comment: C: lncRNA target identification
... I think that you obtained the sequences should be the probe, not the lncRNAs. If you want to get the full-length sequece of lncRNAs, you can download them from some database, such as NCBI, UCSC. You want to find the interaction between lncRNAs and mRNAs, you can calculate the pearson correlation of ...
written 3.0 years ago by Ben50
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Comment: C: lncRNA machine learning
... I have some differentially expressed genes, including mRNAs and lncRNAs. I want to use machien learning to predict the function of lncRNAs ...
written 3.0 years ago by Ben50
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lncRNA machine learning
... I want to use one of machine learning algorithm to predict the function of lncRNAs, Does anyone have any suggestions? Thanks in advance!! ...
rna-seq written 3.0 years ago by Ben50

Latest awards to Ben

Popular Question 23 months ago, created a question with more than 1,000 views. For download tumor and normal data from TCGA
Popular Question 2.0 years ago, created a question with more than 1,000 views. For download tumor and normal data from TCGA

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