User: Sinji

gravatar for Sinji
Sinji2.7k
Reputation:
2,690
Status:
Trusted
Location:
UT Southwestern Medical Center
Last seen:
7 months, 3 weeks ago
Joined:
2 years, 6 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 • 202 results • page 1 of 21 • next >
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Comment: C: stringtie cannot recognize Gencode GTF
... Did you use the appropriate gencode HISAT2 index during mapping? In other words did you create a HISAT2 index using the gencode reference genome fasta file? ...
written 8 months ago by Sinji2.7k
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Comment: C: bedops -u does not work properly
... Great, and yes, bedops is among my most used tools, very powerful! ...
written 8 months ago by Sinji2.7k
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Comment: C: bedops -u does not work properly
... I think the requirements for all bedops operations including `-u` are that the input be sorted prior to being run, however, i've never gotten any errors when giving un-sorted files to bedops, I don't think the `-u` flag changes that, at least not in my experience. I always sort every file I give bed ...
written 8 months ago by Sinji2.7k
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Comment: C: bedops -u does not work properly
... I think you have to include the `--ec` flag for error checking no? ...
written 8 months ago by Sinji2.7k
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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 9 months ago by Sinji2.7k
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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 9 months ago by Sinji2.7k
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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 9 months ago by Sinji2.7k
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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 9 months ago by Sinji2.7k
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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 9 months ago by Sinji2.7k
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Comment: C: Identifying the orientation of a CTCF motif?
... This is excellent, thank you very much! ...
written 11 months ago by Sinji2.7k

Latest awards to Sinji

Popular Question 7 months ago, created a question with more than 1,000 views. For [UPDATE] Thrown into a Bioinformatics Position
Librarian 9 months ago, created a post with more than 10 bookmarks. For Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Popular Question 10 months ago, created a question with more than 1,000 views. For Trim galore terminates with exit signal: '256'
Appreciated 11 months ago, created a post with more than 5 votes. For A: Comparing numbers of ChIP-seq peaks between different sample types
Good Answer 14 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 14 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 14 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
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Basic SAMtools tutorial
Appreciated 16 months ago, created a post with more than 5 votes. For A: Comparing numbers of ChIP-seq peaks between different sample types
Pundit 16 months ago, created a comment with more than 10 votes. For C: SatckExchage/Area51 bioinformatics is back
Gold Standard 16 months ago, created a post with more than 25 bookmarks. For Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Scholar 17 months ago, created an answer that has been accepted. For A: Basic SAMtools tutorial
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Appreciated 17 months ago, created a post with more than 5 votes. For A: Comparing numbers of ChIP-seq peaks between different sample types
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Great Question 19 months ago, created a question with more than 5,000 views. For Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Appreciated 22 months ago, created a post with more than 5 votes. For A: Comparing numbers of ChIP-seq peaks between different sample types
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Popular Question 23 months ago, created a question with more than 1,000 views. For [UPDATE] Thrown into a Bioinformatics Position
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: Basic SAMtools tutorial
Centurion 2.0 years ago, created 100 posts.
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Prophet 2.2 years ago, created a post with more than 20 followers. For Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position

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