Moderator: geek_y

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geek_y8.1k
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Computational Biology. Marie-Curie ESR.

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 humans.

 

Posts by geek_y

<prev • 1,269 results • page 1 of 127 • next >
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Answer: A: Time series analysis from ChIP-Seq data
... You could use same tools. I saw many papers using DESeq2 or edgeR with any king of counts data generated by high throughput sequencin to identify the differences in two different settings. ...
written 21 days ago by geek_y8.1k
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Comment: C: What is the common method(s) to detect eRNAs by using RNA-seq data?
... Sure. cDNA microarray could be used. Thankfully cDNA microarray is not mentioned in the nature reference paper. May be its a mistake that I assumed the OP wants to identify eRNAs from traditional RNA/Seq data. ...
written 21 days ago by geek_y8.1k
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Comment: C: What is the common method(s) to detect eRNAs by using RNA-seq data?
... Thanks, the review you attached states that "Sometimes, by pure chance, the DNA around enhancers may harbor splicing acceptor and donor sites, even perhaps polyadenylation cassettes, in which case the corresponding eRNA becomes spliced, polyadenylated, and stable. **These processed and stable eRNAs, ...
written 22 days ago by geek_y8.1k
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Comment: C: What is the common method(s) to detect eRNAs by using RNA-seq data?
... I guess, its not possible to detect eRNAs by microarray or traditional RNA-Seq data. ...
written 22 days ago by geek_y8.1k
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Comment: C: What is the common method(s) to detect eRNAs by using RNA-seq data?
... Its difficult to find eRNAs through RNA-Seq data. The eRNAs are transcribed at very low levels and are usually do not contains polyA tails. You need to use something like CAGE-Seq to find eRNAs. ...
written 22 days ago by geek_y8.1k
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Comment: C: How to predict the targets of Long noncoding RNA
... If you have large sample size, you could find co-expressed genes. ...
written 5 weeks ago by geek_y8.1k
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Group aware normalisation of genomics data
... I have data ( chromatin and gene expression ) from different tissues, in-house generated and from epigenome roadmap. I certainly have heterogenous samples with in same tissue. I want to normalise all the data so that homogenise the data from different tissues maintaining the variability across tissu ...
qsmooth chip-seq genomics rna-seq written 5 weeks ago by geek_y8.1k
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Comment: C: ATACseq and HiC sequencing
... There are many studies out there using ATAC and HiC. You can check the sequencing depth people usually go for. Best way to sequence ATAC is 50bp PE and usually 60 million reads. If you are interested in generating the TF footprints, you might need hundreds of millions of reads. No idea about Hi-C ...
written 6 weeks ago by geek_y8.1k
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Comment: C: Gene expression values form ENCODE RNA-seq experiments
... If the data is generated by different protocols ( sequencing instrument, stranded/unstranded, single-end/paired-end ) it is possible that the expression levels varies a lot. You need to normalize the data again to use them all together. I am not sure, which normalization methods, but that should be ...
written 7 weeks ago by geek_y8.1k
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Answer: A: single cell RNAseq best tool and work flow
... A very recent workflow of single cell RNA analysis, includes the code and data sets. https://f1000research.com/articles/6-1158/v1 ...
written 8 weeks ago by geek_y8.1k

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Popular Question 3 days ago, created a question with more than 1,000 views. For Google genomics cloud platform ?
Teacher 6 days ago, created an answer with at least 3 up-votes. For A: Is this RNA-seq data reliable?
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Commentator 20 days ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Scholar 9 weeks ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Google genomics cloud platform ?
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Google genomics cloud platform ?
Popular Question 11 weeks ago, created a question with more than 1,000 views. For Google genomics cloud platform ?
Scholar 3 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Scholar 3 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: bioinformatics basic training
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 3 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Scholar 3 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 3 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: pdb to gff?
Scholar 3 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise
Scholar 3 months ago, created an answer that has been accepted. For A: Breaking down the reference genome chromosome-wise

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