User: Sinji

gravatar for Sinji
Sinji2.5k
Reputation:
2,460
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Trusted
Location:
UT Southwestern Medical Center
Last seen:
9 hours ago
Joined:
1 year, 7 months ago
Email:
c*****@ucsd.edu

I am a research assistant at the University of Texas Southwestern Medical Center that only recently began working in computational biology. Most of my work involves the analysis of sequencing data such as ChIP-seq, RNA-seq, and MNase-seq and its visualization. 

Posts by Sinji

<prev • 193 results • page 1 of 20 • next >
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Comment: C: Identifying the orientation of a CTCF motif?
... This is excellent, thank you very much! ...
written 9 hours ago by Sinji2.5k
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Identifying the orientation of a CTCF motif?
... I'm analyzing some CTCF ChIP-seq data, i'm interested in recording the orientation of CTCF sites as they have been shown to have important roles in the underlying biology. I can't seem to find any information on how to do this, despite it being fairly popular. Perhaps just not using the right search ...
chip-seq ctcf written 2 days ago by Sinji2.5k • updated 1 day ago by simon.vanheeringen50
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Comment: C: Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
... Highly recommend deeptools. I discourage the use of NGSPLOT (as you can probably tell in this post) because of the same reasons you seem to be disliking it. HOMER and enrichedHeatmap are great alternatives as well and produce very aesthetically pleasing heatmaps. ...
written 3 months ago by Sinji2.5k
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Answer: A: Snakemake vs. Nextflow: strengths and weaknesses
... I'm a big fan of Nextflow. I've used Snakemake in the past, and it was originally my go-to workflow language, but the built in support for Docker, Singularity, and HPC environments that Nextflow provides just can't be beat. The only downside is you have to use Groovy. ...
written 4 months ago by Sinji2.5k
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Comment: C: Chip-seq peak annotation [Chipseeker]
... Check your ChIP-seq data on IGV and look at a couple of examples of peak calls. Do they mostly fall in the promoter region? If so, then the annotation is probably correct. ...
written 4 months ago by Sinji2.5k
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Comment: C: STAR installation make error
... I'd wonder if it may make more sense to install the Anaconda package manager and then install STAR using that? The command then would be `conda install -c bioconda star`. ...
written 4 months ago by Sinji2.5k
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Answer: A: Peak ident near highly expressed genes
... Probably a more elegant solution available, but: 1. Grab gene locations in BED format. Generally you can do this fairly easily using the [UCSC Table Browser][1] and their `identifiers` option. 2. Use [bedops closest-feature][2] with the `--dist` flag to calculate distances. Make sure to sort files ...
written 4 months ago by Sinji2.5k
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Answer: A: chip-seq analysis and peak annotation
... As another option, you can use ChIPseeker to annotate to the hg38 genome in the exact same way you are probably using hg19 (I assume you are following the Bioconductor guide). All you need to do is download and [install this reference package][1] and use it as your `txdb` object. If you did not use ...
written 4 months ago by Sinji2.5k
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Comment: C: Is annotation of enhancers to nearest gene pointless?
... Gold standard for active enhancers would be: H3K27Ac, H3K4me1, H3K4me2, chromatin accessible, eRNAs, and Pol II. Most studies won't use all these marks, but from what I understand this is considered to be optimal. ...
written 4 months ago by Sinji2.5k
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Answer: A: Is annotation of enhancers to nearest gene pointless?
... I'll also give a bit of information. I work with enhancers quite a lot, and looks like these little suckers will be the focal point of my PhD work as well. It's pretty common knowledge by now that enhancers do not always regulate their most nearby gene, and it's also pretty established that not ALL ...
written 4 months ago by Sinji2.5k

Latest awards to Sinji

Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Comparing numbers of ChIP-seq peaks between different sample types
Epic Question 3 months ago, created a question with more than 10,000 views. For Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Popular Question 3 months ago, created a question with more than 1,000 views. For [UPDATE] Thrown into a Bioinformatics Position
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Basic SAMtools tutorial
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Basic SAMtools tutorial
Appreciated 5 months ago, created a post with more than 5 votes. For A: Comparing numbers of ChIP-seq peaks between different sample types
Pundit 5 months ago, created a comment with more than 10 votes. For C: SatckExchage/Area51 bioinformatics is back
Gold Standard 5 months ago, created a post with more than 25 bookmarks. For Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Scholar 5 months ago, created an answer that has been accepted. For A: Basic SAMtools tutorial
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Appreciated 6 months ago, created a post with more than 5 votes. For A: Comparing numbers of ChIP-seq peaks between different sample types
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Great Question 8 months ago, created a question with more than 5,000 views. For Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Appreciated 11 months ago, created a post with more than 5 votes. For A: Comparing numbers of ChIP-seq peaks between different sample types
Commentator 11 months ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Popular Question 11 months ago, created a question with more than 1,000 views. For [UPDATE] Thrown into a Bioinformatics Position
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Basic SAMtools tutorial
Centurion 13 months ago, created 100 posts.
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Prophet 15 months ago, created a post with more than 20 followers. For Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Guru 16 months ago, received more than 100 upvotes.
Appreciated 16 months ago, created a post with more than 5 votes. For A: Comparing numbers of ChIP-seq peaks between different sample types
Popular Question 16 months ago, created a question with more than 1,000 views. For A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
Voter 17 months ago, voted more than 100 times.

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