User: cbio

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cbio380
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2 years, 10 months ago
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c************@utsouthwestern.edu

Posts by cbio

<prev • 59 results • page 1 of 6 • next >
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Answer: A: Looking for advice on making a grad school decision on bioinformatics/computatio
... I'll be starting my first rotation at UCSD as part of the BISB program in June. So i'll recommend that program! :P It really depends on what type of research you are interested in. ...
written 19 months ago by cbio380
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Answer: A: PhD programs in bioinformatics and genomics
... MIT, University of Washington, Washington University, UCSD, University of Michigan-Ann Arbor, Stanford, CMU are probably good bets. ...
written 2.1 years ago by cbio380
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Comment: C: Bedtools - writing to an output files results in empty files
... Could you format this better? I can't tell what is a line and what is a column. ...
written 2.1 years ago by cbio380
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UCSC Transcriptome File
... I'm looking for a UCSC Trascriptome file for hg19 and hg38 that can be used for psuedo and lightweight aligners like Salmon and Kallisto. I know that the Ensembl annotation can be found easily by looking for the cdna file, but I haven't had much luck in finding a UCSC version. From what I read the ...
ucsc rna-seq transcriptome written 2.2 years ago by cbio380 • updated 2.2 years ago by Devon Ryan86k
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MNase-seq Data Analysis and Processing
... I was hoping someone could point me in the right direction for MNase-seq analysis. I just recently got my hands on a dataset, and after a great deal of looking around, I'm having trouble finding a proper protocol. Could I get a general outline? I know some sequencing types don't like having their f ...
mnase-seq written 2.7 years ago by cbio380 • updated 2.7 years ago by Carlo Yague4.3k
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Comment: C: i want a python script to open a particular research article with its 'doi' (dig
... Must've not locked it or something, i'm able to post here also. EDIT: Unless comments are allowed on other posts. ...
written 2.7 years ago by cbio380
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Identifying -1, NFR, +1 nucleosome arrangement around human TSS annotations
... I'd like to generate a reference-dataset of coordinates for the -1, NFR, +1 nucleosome region surrounding the TSS of genes. I've seen that several papers use datasets such as MNase to do this sort of mapping, but I have not been able to find MNase-seq data in the HCT116 cell line unfortunately. 1) ...
human tss nucleosomes myposts chip-seq tss written 2.7 years ago by cbio380
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Re-creating a heatmap
... I am attempting to re-create a heatmap found in this [article][1] (Figure 3 B, the MNase-seq one). They rank genes / TSS by length of the nucleosome free regions surrounding the TSS. I would like to do something similar using DNase-seq data. I have created many heatmaps before, but I am not typica ...
chipseq heatmap written 2.7 years ago by cbio380 • updated 2.7 years ago by Ryan Dale4.7k
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Answer: A: Whole genome pie chart
... I'm just going to throw out an easy way to do this using the [ChIPseeker][1] R package from Bioconductor. You would first annotate your peaks, and then use the `annoPie` function to achieve your desired results automatically. EDIT: Also mis-read the question. Whoops. [1]: https://bioconductor.or ...
written 2.7 years ago by cbio380
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Comment: C: How do I identify and differentiate between unidirectional and bidirectional pro
... I do not have a separate file for these. What I have currently is a bedtools genomecoverage bedgraph that contains the entire coverage, and is not limited to the -5' option that I generated using: genomeCoverageBed -bg -strand + -ibam $infile -g $genome > outdir/genomecoveragebed/$outfile3 ...
written 2.7 years ago by cbio380

Latest awards to cbio

Popular Question 19 months ago, created a question with more than 1,000 views. For How to generate a pie chart of genomic annotations of ChIP peaks
Popular Question 2.0 years ago, created a question with more than 1,000 views. For MNase-seq Data Analysis and Processing
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: Biotech Graduate aiming for bioinformatics MS leading to PhD
Supporter 2.7 years ago, voted at least 25 times.
Rising Star 2.7 years ago, created 50 posts within first three months of joining.
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Gene Ontology programatically given a list of gene IDs.
Commentator 2.7 years ago, created a comment with at least 3 up-votes. For C: What are some good resources to learn shell script for NGS pipeline development?
Scholar 2.7 years ago, created an answer that has been accepted. For A: Gene Ontology programatically given a list of gene IDs.
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Gene Ontology programatically given a list of gene IDs.
Scholar 2.7 years ago, created an answer that has been accepted. For A: Gene Ontology programatically given a list of gene IDs.
Scholar 2.7 years ago, created an answer that has been accepted. For A: Gene Ontology programatically given a list of gene IDs.
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Gene Ontology programatically given a list of gene IDs.

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