User: paulranum11

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paulranum1130
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Posts by paulranum11

<prev • 24 results • page 1 of 3 • next >
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Comment: C: SPLiT-Seq Demultiplexing a bash tool for extraction of barcoded single cells
... @rainwashautumn I have also noticed this discrepancy with GSM3017260 (SRR6750041). I emailed the authors of the paper months ago about this point but never received a response. I think the issue may be one of two things 1. the dataset is mislabeled in the GEO archive or 2. They performed additional ...
written 28 days ago by paulranum1130
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Comment: C: SPLiT-Seq Demultiplexing a bash tool for extraction of barcoded single cells
... HUGE UPDATE to SPLiT-Seq_Demultiplexing released on Jan_16_2019. An enormous increase in speed was achieved through rewriting steps 1 and 2 in python to make use of hash data structures. Support for a user defined number of mismatches was added. Suggestions, comments, and criticisms welcome. ...
written 4 weeks ago by paulranum1130
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Comment: C: SPLiT-Seq Demultiplexing a bash tool for extraction of barcoded single cells
... The 8bit barcode sequences used in the SPLiT-Seq protocol are redundant between the different barcoding Rounds. You can confirm this here https://drive.google.com/file/d/1l3MkxYVWOPTV5KPpq2uXMLzKOKwVeZyw/view?usp=sharing The barcodes can be redundant because they have flanking sequences used for ...
written 5 weeks ago by paulranum1130
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Answer: A: Seurat: can someone explain how to identify cell types in clusters
... FeaturePlot is a tool that allows you to visualize that distribution of a feature in you tSNE plot. For example if you do: FeaturePlot(object = immune.combined, features.plot = c("CD3D"), min.cutoff = "q9", cols.use = c("lightgrey", "blue"), pt.size = 0.5) You should see the expression level ...
written 3 months ago by paulranum1130
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Answer: A: Problem: "Pair-end" reads scRNA seq data (Drop-seq)
... Hmmmm very strange. Here is a link to the European Nucleotide Archive where you can download their raw .fastq archived dataset from GEO [FASTQ Download Location][1]. Like you said it looks like they only archived one file... I don't know why this would be the case if they truly used paired end seq ...
written 3 months ago by paulranum1130
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Comment: C: Is the Ensembl.org website down today 11/3/2018
... I would expect nothing less from such a courteous and professional commenter. ...
written 3 months ago by paulranum1130
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Comment: C: install libatlas3 without sudo / root access
... I found the `libblas.so` library and linked it using the following command. ln -s ~/anaconda3/pkgs/openblas-0.3.3-ha44fe06_1/lib/libblas.so ~/anaconda3/lib/libblas.so.3 However, I am still getting the same error. Is `~/anaconda3/lib` the correct location to use to make this shared library ava ...
written 3 months ago by paulranum1130
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Comment: C: Is the Ensembl.org website down today 11/3/2018
... Believe it or not dates are formatted differently in different countries. You can read about it [here][1]. [1]: https://www.theguardian.com/news/datablog/2013/dec/16/why-do-americans-write-the-month-before-the-day ...
written 3 months ago by paulranum1130
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Comment: C: install libatlas3 without sudo / root access
... Sorry to make this so tedious... I am having the hardest time figuring out where the openblas library is stored in anaconda. I was able to locate some openblas files using `find ~/anaconda3/ -iname "*openblas*"`. However it is not clear to me which is the blas library that I need. ./pkgs/o ...
written 3 months ago by paulranum1130
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Comment: C: install libatlas3 without sudo / root access
... Thanks for this suggestion! I installed openblas using conda but how do I export the path as LD_LIBRARY_PATH? ...
written 3 months ago by paulranum1130

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Popular Question 2.1 years ago, created a question with more than 1,000 views. For cummeRbund Gene Sets

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