User: Ben

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Ben50
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Posts by Ben

<prev • 46 results • page 1 of 5 • next >
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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 14 days 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 23 days 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 23 days 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 9 weeks ago by Ben50 • updated 9 weeks ago by Alex Reynolds21k
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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 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 3 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 3 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 3 months ago by Ben50
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Comment: C: Combining RNA-Seq and ChIP-Seq
... About the first question, you need to do qRT-PCR and ChIP-qPCR to validate the results you analyzed. Second question, you need to annotate the peaks, then you can obtain a Venn diagram. ...
written 3 months ago by Ben50
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Comment: C: Detection of aberrant mRNA splicing
... you need control samples to compare to tumor RNA-seq ...
written 3 months ago by Ben50

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