User: Sinji

gravatar for Sinji
Sinji3.0k
Reputation:
2,970
Status:
Trusted
Location:
UT Southwestern Medical Center
Last seen:
2 years ago
Joined:
3 years, 11 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 >
1
vote
1
answer
2.3k
views
1
answers
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 2.1 years ago by Sinji3.0k
2
votes
1
answer
587
views
1
answers
Comment: C: bedops -u does not work properly
... Great, and yes, bedops is among my most used tools, very powerful! ...
written 2.1 years ago by Sinji3.0k
0
votes
1
answer
587
views
1
answers
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 2.1 years ago by Sinji3.0k
0
votes
1
answer
587
views
1
answers
Comment: C: bedops -u does not work properly
... I think you have to include the `--ec` flag for error checking no? ...
written 2.1 years ago by Sinji3.0k
0
votes
2
answers
681
views
2
answers
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 2.2 years ago by Sinji3.0k
0
votes
1
answer
746
views
1
answers
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 2.2 years ago by Sinji3.0k
1
vote
0
answers
792
views
0
answers
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 2.2 years ago by Sinji3.0k
1
vote
2
answers
2.5k
views
2
answers
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 2.2 years ago by Sinji3.0k
1
vote
0
answers
3.9k
views
0
answers
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 2.2 years ago by Sinji3.0k
0
votes
1
answer
2.1k
views
1
answers
Comment: C: Identifying the orientation of a CTCF motif?
... This is excellent, thank you very much! ...
written 2.4 years ago by Sinji3.0k

Latest awards to Sinji

Popular Question 2.1 years ago, created a question with more than 1,000 views. For [UPDATE] Thrown into a Bioinformatics Position
Librarian 2.2 years ago, created a post with more than 10 bookmarks. For Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Trim galore terminates with exit signal: '256'
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: Comparing numbers of ChIP-seq peaks between different sample types
Good Answer 2.6 years 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 2.6 years ago, created a question with more than 10,000 views. For Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Popular Question 2.6 years ago, created a question with more than 1,000 views. For [UPDATE] Thrown into a Bioinformatics Position
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Basic SAMtools tutorial
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Basic SAMtools tutorial
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: Comparing numbers of ChIP-seq peaks between different sample types
Pundit 2.8 years ago, created a comment with more than 10 votes. For C: SatckExchage/Area51 bioinformatics is back
Gold Standard 2.8 years ago, created a post with more than 25 bookmarks. For Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Scholar 2.8 years ago, created an answer that has been accepted. For A: Basic SAMtools tutorial
Commentator 2.8 years ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: Comparing numbers of ChIP-seq peaks between different sample types
Commentator 2.8 years ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Great Question 3.0 years ago, created a question with more than 5,000 views. For Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Appreciated 3.3 years ago, created a post with more than 5 votes. For A: Comparing numbers of ChIP-seq peaks between different sample types
Commentator 3.3 years ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Popular Question 3.3 years ago, created a question with more than 1,000 views. For [UPDATE] Thrown into a Bioinformatics Position
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: Basic SAMtools tutorial
Centurion 3.5 years ago, created 100 posts.
Commentator 3.6 years ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position
Prophet 3.7 years ago, created a post with more than 20 followers. For Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
Commentator 3.7 years ago, created a comment with at least 3 up-votes. For C: [UPDATE] Thrown into a Bioinformatics Position

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1593 users visited in the last hour