User: Sinji

gravatar for Sinji
Sinji2.5k
Reputation:
2,530
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Location:
UT Southwestern Medical Center
Last seen:
2 days, 1 hour ago
Joined:
1 year, 9 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 • 198 results • page 1 of 20 • next >
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Answer: A: Detect LINE1 element in NGS data
... HOMER offers a way to download the most recent UCSC reference genome of LINE1 elements (as well as any other transposable elements). ...
written 2 days ago by Sinji2.5k
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Comment: C: How to extract variable nucleotide regions from a list of contigs
... Do you have a reference genome? If you do you could use `bedtools getfasta`. ...
written 2 days ago by Sinji2.5k
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Comment: C: nextflow implementation of grape pipeline
... Essentially this is telling you that you don't have the memory available to run the pipeline on your local machine. I'm not entirely sure what's going on with the cluster error. Have you tried posting a GitHub issue? Shameless plug to my workflow script: https://github.com/c-guzman/cipher-workflow- ...
written 11 days ago by Sinji2.5k
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Comment: C: How Gro-seq identify enhancer RNA?
... This is a difficult question to answer, it's kind of difficult to tease apart eRNA from mRNA when you are looking at intragenic enhancers. This is why a lot of studies focus on intergenic enhancers because they are easy to identify. Typically to be sure you'd have to overlap your GRO-seq to some oth ...
written 12 days ago by Sinji2.5k
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Comment: C: How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files
... To make the plot the center of a peak you have to manually adjust your peak file so that the start and end position are both the middle of the peak. Something like `awk -v OFS='\t' '{print $1, ($2+$3)/2, ($2+$3)/2, $4, $5, $6}' $PEAKFILE > $OUTPUT` ... this is assuming your peak file is a standa ...
written 18 days ago by Sinji2.5k
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Comment: C: Identifying the orientation of a CTCF motif?
... This is excellent, thank you very much! ...
written 8 weeks 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 8 weeks ago by Sinji2.5k • updated 8 weeks ago by simon.vanheeringen110
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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 5 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 6 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 6 months ago by Sinji2.5k

Latest awards to Sinji

Librarian 12 days ago, created a post with more than 10 bookmarks. For Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Trim galore terminates with exit signal: '256'
Appreciated 7 weeks ago, created a post with more than 5 votes. For A: Comparing numbers of ChIP-seq peaks between different sample types
Good Answer 5 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 5 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 5 months ago, created a question with more than 1,000 views. For [UPDATE] Thrown into a Bioinformatics Position
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Basic SAMtools tutorial
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Basic SAMtools tutorial
Appreciated 7 months ago, created a post with more than 5 votes. For A: Comparing numbers of ChIP-seq peaks between different sample types
Pundit 7 months ago, created a comment with more than 10 votes. For C: SatckExchage/Area51 bioinformatics is back
Gold Standard 7 months ago, created a post with more than 25 bookmarks. For Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Scholar 7 months ago, created an answer that has been accepted. For A: Basic SAMtools tutorial
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Appreciated 8 months ago, created a post with more than 5 votes. For A: Comparing numbers of ChIP-seq peaks between different sample types
Commentator 8 months ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Great Question 10 months ago, created a question with more than 5,000 views. For Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Appreciated 13 months ago, created a post with more than 5 votes. For A: Comparing numbers of ChIP-seq peaks between different sample types
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Popular Question 13 months ago, created a question with more than 1,000 views. For [UPDATE] Thrown into a Bioinformatics Position
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Basic SAMtools tutorial
Centurion 15 months ago, created 100 posts.
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Prophet 17 months ago, created a post with more than 20 followers. For Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Commentator 18 months ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Guru 18 months ago, received more than 100 upvotes.

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