User: divya.nandakumar

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7 months ago
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d***************@berkeley.edu

Posts by divya.nandakumar

<prev • 7 results • page 1 of 1 • next >
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Comment: A: Combining viral and host GTF files
... Thanks. It worked for me. ...
written 9 weeks ago by divya.nandakumar20
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Combining viral and host GTF files
... Hi, I have RNA-Seq data from virus infected cell. I would like to get the counts for both viral and host transcripts. I added the virus fasta sequence to the human genome as an additional "chromosome" so that I could align to both the viral and human DNA at the same time. But I don't know how to co ...
alignment rna-seq sequencing written 9 weeks ago by divya.nandakumar20
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Comment: C: RNA Seq analysis of virally infected cells
... I have a doubt about the method you have recommended for DeSeq2. Is there a way to estimate size factors using the entire data (host+viral) but then calculate differential expression for only the viral genes? The way I am doing it right now is using the entire counts (host+viral) that I got from h ...
written 6 months ago by divya.nandakumar20
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Comment: C: RNA Seq analysis of virally infected cells
... Thanks! I will try that ...
written 7 months ago by divya.nandakumar20
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Comment: C: RNA Seq analysis of virally infected cells
... I am not sure I understand. When you say variant, do you mean at the level of DESeq 2 or prior to that? Also, I am not sure I understand how to do the DE only for the viral genes when the counts include both viral + host. Can you help me with that? Thanks! ...
written 7 months ago by divya.nandakumar20
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Comment: C: RNA Seq analysis of virally infected cells
... It is a DNA virus. I dont think that will be a problem for me. But thanks for pointing it out ...
written 7 months ago by divya.nandakumar20
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RNA Seq analysis of virally infected cells
... Hi, I am working with a virally infected cell line. My RNA Seq reads are therefore a combination of host and viral transcripts. I am interested in the viral transcripts that are differentially regulated between the WT and a mutant cell line. I am not sure about the best way to analyze this data. ...
alignment rna-seq written 7 months ago by divya.nandakumar20 • updated 7 months ago by Devon Ryan70k

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