Moderator: geek_y
geek_y ♦ 8.6k
- Reputation:
- 8,630
- Status:
- Trusted
- Location:
- Twitter:
- geek_y
- Scholar ID:
- Google Scholar Page
- Last seen:
- 19 hours ago
- Joined:
- 6 years, 4 months ago
- Email:
- g***********@gmail.com
I work with range of genomic data like transcriptome (RNA-Seq, CAGE-Seq), open chromatin/histone modifications/TF profiles, chromosome contact maps etc to understand tissue specific transcriptional regulation in human genome.
I recently started to work on genetics (eQTLs, caQTLs, hQTLs etc) to understand role of common genetic variants in genome regulation.
Posts by geek_y
<prev
• 1,317 results •
page 1 of 132 •
next >
0
votes
0
answers
131
views
0
answers
... Its not clear.
>1. I total have ~18000 peaks in **condition1**
>
>2. I get overlappeaks ~17000 in both condition(**one bed file**)
>
>3. I get ~13000 peaks only in **condition 1**( another bed file)
Whats the difference between 1 and 3. What is 2 ? ...
written 18 days ago by
geek_y ♦ 8.6k
0
votes
1
answer
98
views
1
answers
... The link is broken, but it doesn't matter for your question.
Any genome browser primarily displays the signal of a ChIP-Seq/RNA-Seq experiment ( and also all other -Seq experiments, variants, peaks, repeat-elements, etc etc etc etc).
For ChIP-Seq, what you see by a bar graph is the signal of a p ...
written 18 days ago by
geek_y ♦ 8.6k
1
vote
1
answer
102
views
1
answers
... You should check and read [FANTOM CAT][1] paper.
[1]: http://fantom.gsc.riken.jp/cat/ ...
written 23 days ago by
geek_y ♦ 8.6k
1
vote
2
answers
120
views
2
answers
... Check [GTEx][1], [human bodymap][2], [epigenome roadmap][3]. Not sure about "eye"
[1]: https://gtexportal.org/home/
[2]: http://www.ensembl.info/2011/05/24/human-bodymap-2-0-data-from-illumina/
[3]: http://www.roadmapepigenomics.org/data/tables/all ...
written 5 weeks ago by
geek_y ♦ 8.6k
0
votes
1
answer
179
views
1
answers
... Hi, for this purpose, you need to use [Coloc][1] which tells if your SNPs are enriched within the genomic locations of any GWAS SNPs of particular trait.
I guess your statement `I have got some GWAS SNPs in my sequencing data` is not correct, because from exome-seq, you might have got SNPs and you ...
written 6 weeks ago by
geek_y ♦ 8.6k
0
votes
1
answer
140
views
1
answers
... What organism and what tissue ? How many samples do you have ? ...
written 7 weeks ago by
geek_y ♦ 8.6k
0
votes
1
answer
202
views
1
answers
... There are some papers, done in specific cell types and disease models:
https://www.nature.com/articles/nature23477?_ga=2.135383345.140789132.1527763165-716992680.1527763162
https://www.cell.com/cell-reports/pdf/S2211-1247(18)30387-5.pdf
https://www.ncbi.nlm.nih.gov/pubmed/29038160
...
written 7 weeks ago by
geek_y ♦ 8.6k
0
votes
1
answer
202
views
1
answers
... I get that, but given the complexity of the genome, complex enhancer regulation, temporal expression of genes, cellular specificity, gene-regulatory networks etc etc, I could not image if someone will be able to do this. I remember a paper about cell survival CRISPR analysis, I will search for that ...
written 7 weeks ago by
geek_y ♦ 8.6k
0
votes
1
answer
202
views
1
answers
... I still did not understand what would be the goal behind this type of experiments. ...
written 7 weeks ago by
geek_y ♦ 8.6k
1
vote
1
answer
202
views
1
answers
... I did not understand this part
> "after targeting a gene, what is the average gene expression change
> for all genes"
It depends on how functional that gene in that particular cell-type. ...
written 7 weeks ago by
geek_y ♦ 8.6k
Latest awards to geek_y
Popular Question
21 days ago,
created a question with more than 1,000 views.
For Generate two haplotypes from bam and vcf
Popular Question
9 weeks ago,
created a question with more than 1,000 views.
For RUVSeq normalisation: Pairing information as a factor
Scholar
9 weeks ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Student
9 weeks ago,
asked a question with at least 3 up-votes.
For What is the best way to handle unmapped reads from RNA-Seq data
Appreciated
9 weeks ago,
created a post with more than 5 votes.
For A: Biostars 3.0 under development. Visitor location is now displayed with a widget.
Commentator
9 weeks ago,
created a comment with at least 3 up-votes.
For C: bioinformatics basic training
Popular Question
10 weeks ago,
created a question with more than 1,000 views.
For RUVSeq normalisation: Pairing information as a factor
Scholar
11 weeks ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Appreciated
11 weeks ago,
created a post with more than 5 votes.
For A: Biostars 3.0 under development. Visitor location is now displayed with a widget.
Good Answer
12 weeks ago,
created an answer that was upvoted at least 5 times.
For A: htseq-count for RNA Seq
Good Answer
5 months ago,
created an answer that was upvoted at least 5 times.
For A: htseq-count for RNA Seq
Great Question
7 months ago,
created a question with more than 5,000 views.
For Where can I download the blast version that includes formatdb ?
Popular Question
8 months ago,
created a question with more than 1,000 views.
For Google genomics cloud platform ?
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: Is this RNA-seq data reliable?
Popular Question
8 months ago,
created a question with more than 1,000 views.
For Google genomics cloud platform ?
Popular Question
8 months ago,
created a question with more than 1,000 views.
For Google genomics cloud platform ?
Commentator
8 months ago,
created a comment with at least 3 up-votes.
For C: bioinformatics basic training
Appreciated
9 months ago,
created a post with more than 5 votes.
For A: Biostars 3.0 under development. Visitor location is now displayed with a widget.
Scholar
10 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 645 users visited in the last hour