User: Ron

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Ron870
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870
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Posts by Ron

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Comment: C: Counting number of base pairs and features in each bed file
... Hi RamRS, I updated my question. I just want to look at the number of base pairs in each bed files.(not features, i Updated it) ...
written 4 days ago by Ron870
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Counting number of base pairs and features in each bed file
... Hello all, Is there any way to count the number of base pairs in each individual bed file? I know we can do this for the intersecting bed files,but want to to do this separately . bedtools intersectBed -a file1.bed -b file2.bed -wo below is the output from the **two bed files using intersect* ...
ngs rna-seq written 4 days ago by Ron870
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Database of Mutations and the associated drugs
... Hi all, I am looking for a database of the clinically relevant mutations that are targetable.(based on mutation level and not gene level) Something similar to what Oncokb has but not sure if its comprehensive? http://oncokb.org/#/actionableGenes Are there any such databases ?Any suggestions would b ...
ngs wes written 6 months ago by Ron870 • updated 6 months ago by Kevin Blighe37k
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Comment: C: Validating driver genes
... What data did you use for finding driver genes? What detection tool you have used?Can you elaborate on this? ...
written 10 months ago by Ron870
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Ratio of samples to do differential expression
... Hi all, I have been doing differential expression for a while.One question that always comes to my mind is regarding the ratio of samples that can be compared between control vs treatment. For e.g. Ideal scenario is to have equal number of controls and treatments. But sometimes when its not possib ...
next-gen rna-seq written 10 months ago by Ron870
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Comment: C: Using Cufflinks for Novel Transcripts
... Hi Seidel, Thanks for your response.I thought about creating a novel Transcript ID and use the necessary exons of interest.But I was not sure since this gene above has FPKM of 0.63 as well as all the exons. So if I just take a few of those exons for novel transcript ,wouldnt the expression be same ...
written 11 months ago by Ron870
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Comment: C: Does Cufflinks report chimeric transcripts/fusion genes?
... You can use STAR-fusion or other fusion softwares for finding fusion genes. ...
written 11 months ago by Ron870
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Using Cufflinks for Novel Transcripts
... Hi all, I am working on transcript level expression from RNAseq using cufflinks after STAR alignment. I am primarily interested in a gene which has a wild type transcript and a novel transcript.The wild type transcript has the coordinateds and is known so it is present in the gencode annotation fil ...
cufflinks rna-seq written 11 months ago by Ron870 • updated 11 months ago by seidel6.7k
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Comment: C: Interpreting GSEA results
... Yes , I also think the same . that in their experiment the genes are downregulated when RB1 and RB2 are knocked out, but in our data those genes are up regulated. So can we say that still our data is **related** to those **two genes** being **knocked out / down** ,despite of the fact that the genes ...
written 14 months ago by Ron870
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Comment: C: Interpreting GSEA results
... The data is normalized by DESEQ package while doing differential expression.Thanks for your comment ,however thats not what I asked. I just want to know if my results from differential expression analysis - how they relate with this specific pathway based on the enrichment plot ? ...
written 14 months ago by Ron870

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