User: Ben

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Ben50
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Posts by Ben

<prev • 43 results • page 1 of 5 • next >
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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 10 days ago by Ben50 • updated 10 days ago by Alex Reynolds20k
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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 4 weeks 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 5 weeks 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 5 weeks 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 5 weeks 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 7 weeks 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 8 weeks ago by Ben50
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Comment: C: TCGA & METABRIC Breast Cancer Subtype Survival Curve
... Do you know how to download tumor and normal RNA-seq samples from TCGA? ...
written 9 weeks ago by Ben50
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Comment: C: Creating reproducible peak regions from multiple ChIP-seq studies
... Do you want to obtain overlapping peaks from different ChIP-seq? ...
written 10 weeks ago by Ben50
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Comment: C: What's Pathway Enrichment Analysis?
... I remember that enrichment analysis was analyzed with Fisher`s exact test ...
written 10 weeks ago by Ben50

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