User: landrjos

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landrjos10
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Posts by landrjos

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Advice on Normalizing Baseline from NGS.Plot.R
... Here is the link to the image. ![enter image description here][1] [1]: http://oi64.tinypic.com/1ibgup.jpg ...
written 12 months ago by landrjos10 • updated 12 months ago by ATpoint26k
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Advice on Normalizing Baseline from NGS.Plot.R
... Hi All, I was need some advice on how to present some aggregate plot data. I have 2 categories of genes that I want to analyze. When I look at the enrichment at the TSS of these 2 gene categories for a factor from a ChIP-Seq data set I get the following result. ![NGS plot peaks showing differenc ...
R chip-seq written 12 months ago by landrjos10
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Comment: C: Effective Genome Size for Masked MM9 36 bp reads
... Hi All, A common effective genome size used for the unmasked MM9 genome is 2,150,570,000. Would masking reduce this to 58% because 58% of the genome is non repetitive. Is it that simple? Joe ...
written 12 months ago by landrjos10
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Effective Genome Size for Masked MM9 36 bp reads
... Hi All, I was wondering if anyone knows the effective genome size for the masked MM9 build using 36 bp reads with 1 mismatch? Do I need to determine this with software? If so how would I do it. I need this number to do a GC correction of my ChIP-Seq data. Best, Joe ...
genome chip-seq written 12 months ago by landrjos10
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Comment: C: R code for Differential Gene Expression
... Hi Kevin, I was wondering if you could provide some feedback on my EDGER code, and its application to my specific experiment as outlined below. Any help would be appreciated. Best, Joe ...
written 13 months ago by landrjos10
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Comment: C: R code for Differential Gene Expression
... Hi Kevin, I have 2 conditions wild type (WT) and knockout (KO). I would like determine if the differential gene expression observed between WT and KO segregate the two groups using clustering or by a denditogram. Basically just as you mentioned in your comment above. I removed the correlation mat ...
written 13 months ago by landrjos10 • updated 13 months ago by Kevin Blighe52k
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Comment: A: R code for Differential Gene Expression
... Hi Kevin, Regarding point 1....can you show me the changes you would suggest? Can you make the edits and paste them back into the field so that I can see how you make the changes.... Best, Joe ...
written 13 months ago by landrjos10
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Comment: A: R code for Differential Gene Expression
... Hi Kevin, The goal was not to determine differences in splicing. I used rMATs to do that. I am just looking for differential transcript abundance. I just want to make sure my normalization and F-test sequence is valid. I get a reasonable number of genes, which reasonable pValues, so I don't thi ...
written 13 months ago by landrjos10
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R code for Differential Gene Expression
... Hi All, I was wondering if you could look over my R code for differential gene expression using EdjeR. I am looking to determine differential gene expression between wild type (WT) cells and knockout cells (KO). Three biological replicates were grown for each cell line and RNA was harvested. The ...
rna-seq written 13 months ago by landrjos10
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Splitting Odd and Even Reads from FastQ to Seperate Output Files
... Hi All, I have a bioinformatics question. I would like to partition a fastq file into 2 separate output files with odd reads (lines 1-4, 9-12, etc....) into a odd output file (file1) and even reads (lines 5-8, 13-16) into a even output file (file2). Does anyone know a Split command which would do ...
sequence written 16 months ago by landrjos10 • updated 16 months ago by 5heikki8.6k

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