User: jrleary

gravatar for jrleary
jrleary10
Reputation:
10
Status:
New User
Location:
Lineberger Comprehensive Cancer Center
Last seen:
22 hours ago
Joined:
2 weeks, 5 days ago
Email:
j******@live.unc.edu

Lowly undergrad research assistant running bulk / single cell RNAseq and downstream analysis. Focused on pancreatic cancer. 

Posts by jrleary

<prev • 11 results • page 1 of 2 • next >
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Comment: C: C++ versus Python for dimension reduction / clustering speed?
... The Rtsne package that everyone uses is an ```Rcpp``` implementation of the Barnes-Hut fast t-SNE written by Laurens van der Maaten. The question was less about the algorithm itself and more about the speed of computation of C++ vs. R, since C++ is a lower level language. ...
written 1 day ago by jrleary10
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Comment: C: C++ versus Python for dimension reduction / clustering speed?
... Yes, I'm aware of the various implementations of both t-SNE and UMAP and their benefits / drawbacks. My interest is in reducing the computation time of running these algorithms several times, since R is memory-greedy and slow. I plan on simply calling the C++ code provided on van der Maaten's GitHub ...
written 1 day ago by jrleary10
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Answer: A: Trimming Adapters for RNA-SEQ (Quality Check)
... The first poster gave a great response, but I'd posit that ```skewer``` is also a great option for read trimming. You can use a specific adapter or set of adapters as input, and it's wicked fast. The downside is that there's not a ton of documentation available, but if you decide to go down that pat ...
written 1 day ago by jrleary10
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C++ versus Python for dimension reduction / clustering speed?
... So I've decided to write a program to compute dimension reduction and potentially clustering specifically for single cell RNAseq. I got tired of running PCA/t-SNE in R, where I do most of my downstream analysis, since t-SNE specifically takes such a long time to run. Typically I'll run t-SNE with se ...
python dimension reduction c++ written 1 day ago by jrleary10 • updated 1 day ago by Mensur Dlakic2.4k
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Can cell ranger count take a folder of only .fastq.gz as input?
... I'm attempting to run cellranger count on some fastq files provided to me by a colleague from a different lab. Every other time I've processed single cell data I've done every step myself, from sequencing -> downstream analysis. Typically when running cellranger count I specify the subdirectory t ...
cellranger scrnaseq written 5 days ago by jrleary10 • updated 5 days ago by swbarnes27.0k
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Comment: C: How much memory / how many cores should I request for peak calling?
... Ah yes, I had kind of assumed that MACS2 had multithread support but according to [this feature request on their GitHub][1] it isn't supported yet. Guess I'll just request one core and a ton of memory. Thanks! [1]: https://github.com/taoliu/MACS/issues/334 ...
written 10 days ago by jrleary10
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How much memory / how many cores should I request for peak calling?
... I've never run ChIPseq before, so I've been writing a pipeline from scratch to perform all the necessary read trimming, alignment, etc. I've successfully gotten to the peak calling step, which I will be performing using MACS2. My question is, how much memory and how many cores should I request from ...
slurm chip-seq written 10 days ago by jrleary10 • updated 10 days ago by genomax75k
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Comment: C: How should I use skewer to trim paired end reads?
... I'll give both of these a look and compare their performance with that of skewer now that I've got it working. Thanks for the options. ...
written 19 days ago by jrleary10
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Comment: C: How should I use skewer to trim paired end reads?
... This rectified the problem, thank you! ...
written 19 days ago by jrleary10
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Comment: C: How should I use skewer to trim paired end reads?
... I like skewer because of fast it is, but I'm open to using other tools if the documentation / speed tradeoff is worth it ...
written 19 days ago by jrleary10

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