Moderator: geek_y

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geek_y8.6k
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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

<prev • 1,317 results • page 1 of 132 • next >
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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 18 days ago by geek_y8.6k
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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 18 days ago by geek_y8.6k
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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 23 days ago by geek_y8.6k
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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 5 weeks ago by geek_y8.6k
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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 6 weeks ago by geek_y8.6k
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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 7 weeks ago by geek_y8.6k
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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 7 weeks ago by geek_y8.6k
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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 7 weeks ago by geek_y8.6k
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Comment: C: Genome-wide CRISPR/Cas9 and gene expression?
... I still did not understand what would be the goal behind this type of experiments. ...
written 7 weeks ago by geek_y8.6k
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Comment: C: Genome-wide CRISPR/Cas9 and gene expression?
... 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_y8.6k

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