Moderator: geek_y
geek_y ♦ 8.8k
- Reputation:
- 8,760
- Status:
- Trusted
- Location:
- Twitter:
- geek_y
- Scholar ID:
- Google Scholar Page
- Last seen:
- 1 week, 1 day ago
- Joined:
- 6 years, 8 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
• 1,320 results •
page 1 of 132 •
next >
1
vote
2
answers
118
views
2
answers
... Quantify the genes from both technical replicates and check the correlation between two samples. PCA might not give a good idea between technical replicates. Its good for biological replicates, as it takes only top 500 or 1000 genes. "Bad quality samples" either mean the initial RNA is of poor quali ...
written 4 weeks ago by
geek_y ♦ 8.8k
1
vote
1
answer
194
views
1
answers
... It depends. You could simply start with QTLtools or MatrixQTL which are easy fast to run. You could also go to more robust pipelines like RASQUAL which also models for allelic counts. ...
written 3 months ago by
geek_y ♦ 8.8k
2
votes
1
answer
194
views
1
answers
... 50 individuals with transcriptome would be enough to get decent number of eQTLs. Which tissue are you working with ? Ideally you should genotye the DNA from these 50 individuals and then do imputation to get more SNPs and then run them through eQTL pipelines- ...
written 3 months ago by
geek_y ♦ 8.8k
0
votes
0
answers
240
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 4 months ago by
geek_y ♦ 8.8k
0
votes
1
answer
207
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 4 months ago by
geek_y ♦ 8.8k
1
vote
1
answer
172
views
1
answers
... You should check and read [FANTOM CAT][1] paper.
[1]: http://fantom.gsc.riken.jp/cat/ ...
written 4 months ago by
geek_y ♦ 8.8k
1
vote
2
answers
188
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 months ago by
geek_y ♦ 8.8k
0
votes
1
answer
281
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 5 months ago by
geek_y ♦ 8.8k
0
votes
1
answer
214
views
1
answers
... What organism and what tissue ? How many samples do you have ? ...
written 5 months ago by
geek_y ♦ 8.8k
0
votes
1
answer
355
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 5 months ago by
geek_y ♦ 8.8k
Latest awards to geek_y
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Generate two haplotypes from bam and vcf
Popular Question
6 months ago,
created a question with more than 1,000 views.
For RUVSeq normalisation: Pairing information as a factor
Scholar
6 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Student
6 months 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
6 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.
Commentator
6 months ago,
created a comment with at least 3 up-votes.
For C: bioinformatics basic training
Popular Question
6 months ago,
created a question with more than 1,000 views.
For RUVSeq normalisation: Pairing information as a factor
Scholar
6 months ago,
created an answer that has been accepted.
For A: Breaking down the reference genome chromosome-wise
Appreciated
6 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.
Good Answer
6 months ago,
created an answer that was upvoted at least 5 times.
For A: htseq-count for RNA Seq
Good Answer
8 months ago,
created an answer that was upvoted at least 5 times.
For A: htseq-count for RNA Seq
Great Question
11 months ago,
created a question with more than 5,000 views.
For Where can I download the blast version that includes formatdb ?
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Google genomics cloud platform ?
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: Is this RNA-seq data reliable?
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Google genomics cloud platform ?
Popular Question
12 months ago,
created a question with more than 1,000 views.
For Google genomics cloud platform ?
Commentator
12 months ago,
created a comment with at least 3 up-votes.
For C: bioinformatics basic training
Appreciated
13 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.
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 936 users visited in the last hour