User: phosphodiester_bond

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Posts by phosphodiester_bond

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Binding affinity DB out there?
... I know this is a long shot, but... Say you have a compound (could be a drug, but not necessarily), and a particular protein of interest. What is currently the simplest way to obtain some quantitative measure of binding affinity between them? Is there an up-to-date database where ligand/receptor aff ...
binding curation affinity written 14 months ago by phosphodiester_bond40 • updated 13 months ago by Biostar ♦♦ 20
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Comment: C: Processing ATAC-seq data after peak calling
... Hi! I would need to look at the documentation carefully, but at first pass it seems these are two different tools and chromVAR is more focused on comparing the ATAC-seq signal itself between experiments, rather than the estimated levels of TF activity between the two datasets. It looks like it prov ...
written 17 months ago by phosphodiester_bond40
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Answer: A: Processing ATAC-seq data after peak calling
... Hi Anaïs, If you'd like to analyze differences in transcription factor activity between the two groups, we developed a tool to do this using your called peaks from ATAC-seq: https://biof-git.colorado.edu/dowelllab/DAStk More info here: http://www.mdpi.com/1420-3049/23/5/1136 Good luck! ...
written 18 months ago by phosphodiester_bond40
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Comment: C: What is the best pipeline step to merge replicates?
... Thank you, I see now how this is probably not something with a generalizable solution (which is why I kept my original post intentionally vague). ...
written 20 months ago by phosphodiester_bond40
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Comment: C: What is the best pipeline step to merge replicates?
... Sorry about the extreme vagueness, I just edited my original post. This is ATAC-seq data that I'm pulling from GEO accessions, all uploaded by other labs. Most of these are biological replicates. ...
written 20 months ago by phosphodiester_bond40
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What is the best pipeline step to merge replicates?
... Based on your experience, at which point would you recommend merging the reads from multiple ATAC-seq replicates (biological replicates, for the most part)? And most importantly, why? I saw at Encode they first process the samples independently up to the BAM files, and merge all BAM files using sa ...
pipeline sequencing written 20 months ago by phosphodiester_bond40 • updated 20 months ago by Friederike5.3k
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Answer: A: What are the best tools for differential detection between ATAC-seq samples?
... Once you have your peaks for each condition, you can try DAStk, a tool recently put out for that purpose: https://biof-git.colorado.edu/dowelllab/DAStk ...
written 21 months ago by phosphodiester_bond40
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Answer: A: Differential Peak Expression in ATAC-seq data
... You can try DAStk, a tool recently put out for that purpose: https://biof-git.colorado.edu/dowelllab/DAStk ...
written 21 months ago by phosphodiester_bond40
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Comment: C: How To Get The Sequence Of A Genomic Region From Ucsc?
... Thanks, this is really handy!! ...
written 2.4 years ago by phosphodiester_bond40
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Comment: C: liftOver narrowPeak file
... Just curious if you've ever figured this out. I'm wondering the same for GRCh38-mapped narrowPeak files to hg19. I suspect getting rid of the offending columns is not advisable. ...
written 2.7 years ago by phosphodiester_bond40

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