User: shenli.sam
shenli.sam • 150
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Posts by shenli.sam
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... A bioinformatician position is open in Dr. Shen’s group at the Icahn School of Medicine at Mount Sinai in New York City. This is a permanent staff position. Consequently you’ll enjoy the full benefits as a Mount Sinai employee. Our research mainly focuses on bioinformatic analysis of transcriptomic ...
written 27 days ago by
shenli.sam • 150
• updated
27 days ago by
genomax ♦ 28k
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... As of today, the position is still open. Interested persons please send your resume. ...
written 4 weeks ago by
shenli.sam • 150
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... A bioinformatician position is open in Dr. Shen’s group at the Icahn School of Medicine at Mount Sinai in New York City. This is a permanent staff position. Consequently you’ll enjoy the full benefits as a Mount Sinai employee. Our research mainly focuses on bioinformatic analysis of transcriptomic ...
written 4 months ago by
shenli.sam • 150
3
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... A bioinformatician position is open in Dr. Shen’s group at the Icahn School of Medicine at Mount Sinai in New York City. This is a permanent staff position. Consequently you’ll enjoy the full benefits as a Mount Sinai employee. Our research mainly focuses on bioinformatic analysis of transcriptomic ...
written 8 months ago by
shenli.sam • 150
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... Dear Honey, I'm sorry that you are having this trouble. We do have a local instance of ngs.plot at Mt. Sinai but it is really difficult to make it public due to school policy. ngs.plot is more actively being developed as a command line tool. The Galaxy version is kind of outdated. If you don't mind ...
written 3.9 years ago by
shenli.sam • 150
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... Normalization by sequencing depth (i.e. total read count) is probably the simplest approach but is widely used. There are some drawbacks with this approach. For example, if the signal-to-noise ratio is very different between two libraries, one library is going to contain more background reads than t ...
written 3.9 years ago by
shenli.sam • 150
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... Have you calculated coverage for your bisulfite-seq data? If yes, IGV can certainly draw a plot like that.
If you want global visualization for your ChIP-seq at functional genomic regions, consider ngs.plot. It generate beautiful figures in vector-based format, which can be loaded into an image ed ...
written 3.9 years ago by
shenli.sam • 150
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... You can use diffReps. It is an automated pipeline for ChIP-seq differential analysis. Since you don't have replicates, you can choose G-test (recommended) or Chi-square test. diffReps has implemented them all.
...
written 3.9 years ago by
shenli.sam • 150
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... MAnorm only considers the intensity or confidence of a peak but not its shape. Depending on the variation of the replicates, the peaks may have different sizes: some are longer, some are shorter and some are shifting towards up- or down-stream. This is OK if you just want to get a consensus peak lis ...
written 3.9 years ago by
shenli.sam • 150
2
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... There is a downside with this kind of approach. Given the variation between different replicates, it can become very difficult to define the so called "consensus" peak. You may come up with various strategies but no one can tell which gives you the best result. In addition, +/-100bp probably works w ...
written 3.9 years ago by
shenli.sam • 150
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3.9 years ago,
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For A: Differential Peaks Between Replicates
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