Moderator: geek_y

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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

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Comment: C: How to approach QTL for transcriptomic data?
... 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 8 weeks ago by geek_y8.7k
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Comment: C: How to approach QTL for transcriptomic data?
... 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 8 weeks ago by geek_y8.7k
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Comment: C: macs2 find different binding sites
... 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 11 weeks ago by geek_y8.7k
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Answer: A: Question on BIGWIG tracks from Chip Seq experiments
... 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 11 weeks ago by geek_y8.7k
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Answer: A: Separate non-coding RNA from total RNA list
... You should check and read [FANTOM CAT][1] paper. [1]: http://fantom.gsc.riken.jp/cat/ ...
written 12 weeks ago by geek_y8.7k
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Answer: A: Best database for human mRNA expression information from different tissues?
... 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 3 months ago by geek_y8.7k
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Answer: A: Disease/Trait SNPs Enrichment Analysis
... 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 3 months ago by geek_y8.7k
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Comment: C: Noncoding RNA and protein coding gene co expression
... What organism and what tissue ? How many samples do you have ? ...
written 3 months ago by geek_y8.7k
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Answer: A: Genome-wide CRISPR/Cas9 and gene expression?
... 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 3 months ago by geek_y8.7k
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Comment: C: Genome-wide CRISPR/Cas9 and gene expression?
... 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 3 months ago by geek_y8.7k

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