User: cbio

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cbio370
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1 year, 11 months ago
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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 8 months ago by cbio370
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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 14 months ago by cbio370
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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 14 months ago by cbio370
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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 15 months ago by cbio370 • updated 15 months ago by Devon Ryan73k
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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 21 months ago by cbio370 • updated 21 months ago by Carlo Yague3.5k
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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 21 months ago by cbio370
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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 21 months ago by cbio370
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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 21 months ago by cbio370 • updated 21 months ago by Ryan Dale4.6k
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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 21 months ago by cbio370
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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 21 months ago by cbio370

Latest awards to cbio

Popular Question 13 months ago, created a question with more than 1,000 views. For MNase-seq Data Analysis and Processing
Appreciated 20 months ago, created a post with more than 5 votes. For A: Biotech Graduate aiming for bioinformatics MS leading to PhD
Supporter 21 months ago, voted at least 25 times.
Rising Star 21 months ago, created 50 posts within first three months of joining.
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Gene Ontology programatically given a list of gene IDs.
Commentator 21 months 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 21 months ago, created an answer that has been accepted. For A: Gene Ontology programatically given a list of gene IDs.
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Gene Ontology programatically given a list of gene IDs.
Scholar 22 months ago, created an answer that has been accepted. For A: Gene Ontology programatically given a list of gene IDs.
Scholar 22 months ago, created an answer that has been accepted. For A: Gene Ontology programatically given a list of gene IDs.
Teacher 22 months 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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