User: stephen66

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stephen6630
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United States
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2 years, 7 months ago
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2 years, 11 months ago
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Posts by stephen66

<prev • 5 results • page 1 of 1 • next >
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plotMA in DEseq2
... Dear Community, Sorry if this question is too simple. Would like to how to use plotMA to plot the unshrunken log2 fold changes in result table after calling, results(dds, addMLE=TRUE)  ? Many thanks.   Stephen ...
deseq2 written 2.6 years ago by stephen6630 • updated 2.6 years ago by Michael Love14k
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Answer: A: How to analyze a known fusion gene expression in RNAseq
... Thanks. However, I am wondering it this approach works. Since I am thinking that the original fastq reads of that fusion gene were not even mapped to the reference genome as the reference genome does not have the fusion sequence, so the reads of fusion gene likely would not even appear in bam files. ...
written 2.6 years ago by stephen6630
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How to analyze a known fusion gene expression in RNAseq
... Dear All, I know pretty well the RNAseq workflow using GenomicAlignment and DEseq2 to analyse RNAseq expression. Now I want to calculate one known fusion gene expression in my two RNAseq samples which are from cancer cells that I know have the fusion gene. So I know this fusion gene sequence, but I ...
rnaseq fusion genes written 2.6 years ago by stephen6630
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how to get genomic coordinates for a list of genes
... Dear All, I want to get genomic coordinates for a list of human genes. I don't quite know where to start and which package(s) to use. Could you guide me which bioconductor packages to use so I can go read those manual by myself. Thanks a lot!   Stephen   ...
genomicranges written 2.8 years ago by stephen6630 • updated 2.8 years ago by Sean Davis21k
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how can I tell if a RNAseq BAM file is paired end or single end ?
... Dear All, I have some RNAseq BAM files left from previous labmates. Is there a quick way to tell are these BAM files paired end or not ? Many Thanks!! Stephen ...
ngs bam written 2.9 years ago by stephen6630 • updated 2.9 years ago by Sonali Arora360

Latest awards to stephen66

Popular Question 2.6 years ago, created a question with more than 1,000 views. For how can I tell if a RNAseq BAM file is paired end or single end ?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For how can I tell if a RNAseq BAM file is paired end or single end ?
Popular Question 2.6 years ago, created a question with more than 1,000 views. For how to get genomic coordinates for a list of genes

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