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 19 days ago by benjyrolls70
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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 8 weeks 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 8 weeks ago by benjyrolls70 • updated 8 weeks ago by prakash30
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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 8 weeks ago by benjyrolls70 • updated 8 weeks 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 10 weeks ago by benjyrolls70 • updated 10 weeks ago by Devon Ryan71k
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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 12 weeks ago by benjyrolls70 • updated 12 weeks ago by theobroma22980
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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 12 weeks 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 12 weeks 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 12 weeks 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 12 weeks ago by benjyrolls70

Latest awards to benjyrolls

Supporter 3 months ago, voted at least 25 times.
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Cancer expression data sets

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