User: Ben

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Ben50
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Posts by Ben

<prev • 48 results • page 1 of 5 • next >
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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 5 months 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 7 months 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 9 months 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 9 months 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 9 months 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 11 months ago by Ben50 • updated 11 months ago by Alex Reynolds24k
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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 12 months 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 12 months 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 12 months ago by Ben50
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Comment: C: Gene Ontology Analysis
... Did not you obtain any GO terms? if so, you cany try other tools, such DAVID, goprofile. ...
written 12 months ago by Ben50

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Popular Question 11 days ago, created a question with more than 1,000 views. For download tumor and normal data from TCGA

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