User: benjyrolls

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benjyrolls70
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Posts by benjyrolls

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Explanation of BETA output
... Hello, I have an RNA-Seq experiment( OCT4 KO vs WT mouse) and ChIP-Seq experiment ( WT vs OCT4 enriched ChIP sample). I have analysed my Cuffdiff differential expressed gene output from my RNA-Seq with my OCT4 enriched peaks bed file using [Cistrome BETA][1] and obtained [this output][2] am tryi ...
beta chip-seq rna-seq data integration written 13 hours ago by benjyrolls70
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BETA for RNA-Seq and ChIP-Seq Data Integration
... Hello, I have a Cuffdiff file output from RNA-Seq study and a bed file from MACS from my ChIP-Seq study. RNA-Seq study involved a Knockdown of p53 vs wild type mouse and chiPseq study involved wt vs p53 enriched chip. I am using the public Cistrome server [here][1] The default gene expression fi ...
beta chip-seq rna-seq data integration written 2 days ago by benjyrolls70 • updated 1 day ago by Biostar ♦♦ 20
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Evaluating an RNA-Seq/ChIP-Seq Scientific finding
... Hello I would like to evaluate the robustness of my scientific findings done in RNA-Seq and ChIP-Seq. Assuming I found some genes (Gene1, Gene2,Gene3 etc) being targeted by p53 transcription factor. for the scientific findings I have thought about checking result with other experiments to make sure ...
next-gen chip-seq rna-seq written 14 days ago by benjyrolls70 • updated 14 days ago by Devon Ryan70k
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CummeRbunds Model fit plot
... Hi am using cummeRbund for fRNASeq expression plot analysis and using their [manual][1] I came out with this [model fit plot][2]. could someone explain what this means ? Thanks [1]: http://compbio.mit.edu/cummeRbund/manual_2_0.html#tth_sEc5 [2]: https://ibb.co/mpGCVQ ...
cummerbund rna-seq written 26 days ago by benjyrolls70 • updated 26 days ago by theobroma22890
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Comment: C: Reads partly within an exon
... if I did pathway analysis for genes targeted by SOX2 and found those genes also present in RNA-Seq experiment is this also right ? ...
written 27 days ago by benjyrolls70
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Comment: C: Reads partly within an exon
... > Consider choosing a read count methodology that ignores such reads Am using Cuffdiff am not sure if this can do this ? > > we don't know if there is a batch effect (i.e. some samples are more > affected than others). I need to do further analysis to see this. > > > You ...
written 27 days ago by benjyrolls70
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Comment: C: Reads partly within an exon
... If its genomic DNA contamination what are the effects on the experimental outcome? ...
written 27 days ago by benjyrolls70
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Comment: C: Reads partly within an exon
... > we don't know what the aim of your analysis is. The aim of the analysis is to find the effect of SOX2 knockout in the stomach ...
written 27 days ago by benjyrolls70
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Comment: C: Reads partly within an exon
... yes I have is there a portion I could check to find the coverage and figure whats going on. b[rowser view][1] Assuming these are genomic DNA contamination, should this a cause for concern compared with the number of reads 84% that are within an exon ? [1]: https://ibb.co/cnVrn5 ...
written 28 days ago by benjyrolls70
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Comment: C: Reads partly within an exon
... Its a quantification summary of all the reads for all the samples and their replicates ...
written 28 days ago by benjyrolls70

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Supporter 5 weeks ago, voted at least 25 times.
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Cancer expression data sets

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