User: benjyrolls

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benjyrolls70
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Posts by benjyrolls

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Bioinformatics Tools for Novel Gene Search
... I am trying to find novel genes in my RNA-Seq and ChIP-Seq data sets using https://blast.ncbi.nlm.nih.gov/Blast.cgi and following this [publication][1], bu am very new to this tool. Could somene explain how to about this, or suggest another tool to find novel genes from my data please? [1]: ...
chip-seq rna-seq written 11 weeks ago by benjyrolls70 • updated 14 days ago by Biostar ♦♦ 20
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Comment: C: BETA for RNA-Seq and ChIP-Seq Data Integration
... Thanks for the reply. I found out I had to delete the header in the Cuffdiff output before the web one had to work. The --gname in the command line works as well. ...
written 3 months ago by benjyrolls70
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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 3 months ago by benjyrolls70 • updated 3 months ago by prakash100
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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 4 months ago by benjyrolls70 • updated 3 months 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 4 months ago by benjyrolls70 • updated 4 months ago by Devon Ryan74k
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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 4 months ago by benjyrolls70 • updated 4 months ago by theobroma221.0k
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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 4 months 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 4 months 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 4 months 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 4 months ago by benjyrolls70

Latest awards to benjyrolls

Supporter 5 months ago, voted at least 25 times.
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Cancer expression data sets

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