User: shenli.sam

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shenli.sam100
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Posts by shenli.sam

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Job: Looking for a bioinformatician to work on NGS analysis in epigenomics, Ican Scoll of Medicine at Mount Sinai, NY, USA
... 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 ...
chip-seq epigenomics ngs analysis rna-seq job written 17 days ago by shenli.sam100 • updated 17 days ago by genomax220k
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Job: Looking for a bioinformatician to work on NGS analysis in epigenomics (New York City)
... 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 ...
next-generation sequencing job bioinformatician written 4 months ago by shenli.sam100
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Comment: C: Looking For A Public Instance Of Galaxy That Has The "Ngs.Plot" Tool Installed
... 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 The Galaxy version is kind of outdated.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 3.5 years ago by shenli.sam100
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Answer: A: How To Do Normalization Of Two Chip-Seq Data?
... 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 3.6 years ago by shenli.sam100
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Answer: A: Visualizing Chip-Seq And Bis-Seq (Dna Methylation) Data
... 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 3.6 years ago by shenli.sam100
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Answer: A: Differential Histone Chip-Seq Analysis Without Replicates
... 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 3.6 years ago by shenli.sam100
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Comment: C: Differential Peaks Between Replicates
... 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 3.6 years ago by shenli.sam100
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Comment: C: Differential Peaks Between Replicates
... 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 3.6 years ago by shenli.sam100
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Answer: A: Differential Peaks Between Replicates
... diffReps can analyze your ChIP-seq data in an automated pipeline. In addition to finding differential sites, it can also identify hotspots and annotate your differential sites/peaks to genes or heterochromatic regions. diffReps does not depend on peak calling, though. This actually provides you with ...
written 3.6 years ago by shenli.sam100
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Comment: C: Need Advice On The Correct Usage For The Genome Structure Correction Statistical
... Hi Chris, when you see a low p-value for your shuffled BED file, did you see a negative or positive Z-score? ...
written 4.6 years ago by shenli.sam100

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Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Differential Peaks Between Replicates

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