User: akh22

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akh2230
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United States
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4 days, 5 hours ago
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4 years, 8 months ago
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a****@pitt.edu

Posts by akh22

<prev • 28 results • page 1 of 3 • next >
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Answer: A: Loading 10x data into Monocle 3
... I figured it out. It was simple. CellRanger uses mm10 as a mouse ref, genome, and all I have to do is to change the name of folder, GRCm38 to mm10. This did it. ...
written 15 days ago by akh2230
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Comment: C: Loading 10x data into Monocle 3
... Thanks. I don't see any posts in their google group, and that's why I posted a question here, but I sent email to monocle-user to see if I can get faster response. Thanks. ...
written 18 days ago by akh2230
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Comment: C: Loading 10x data into Monocle 3
... Ok Here we go; ![Directory Structure 1][1] ![Directory Structure 2 ][2] [1]: https://i.ibb.co/NN5ZTCQ/Aura-2019-06-28-10-50-28.png [2]: https://i.ibb.co/dmmfkcs/Aura-2019-06-28-10-56-31.png and the location of monocle/ is `/Volumes/Aura/monocle` ...
written 18 days ago by akh2230
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Comment: C: Loading 10x data into Monocle 3
... They are the right paths. /Volumes/Documents/ahoji as a part of "/Volumes/Documents/ahoji/Desktop/Aura 2019-06-28 10-50-28.png" is a path to my image file showing a directory structure within Volumes/Aura/monocle/ but for some reasons the image was not loaded. Originally, I had the following dire ...
written 18 days ago by akh2230 • updated 18 days ago by RamRS22k
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Loading 10x data into Monocle 3
... Hi, I've been struggling to load our mouse 10x data into Monocle3 by using; cds10x<-load_cellranger_data("/Volumes/Aura/monocle/") However, I get this error message; Error in get_genome_in_matrix_path(matrix_dir, genome) : Multiple genomes found; please specify one. Genomes ...
R next-gen 10xdata monocle3 rna-seq written 18 days ago by akh2230
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Comment: C: Bioinformatics Workstation Suggestions
... My plan initially was to build a Linux box with Ubuntu or KDE but nobody in my lab wanted to deal with command line stuff too much so I decided to build a Window machine instead. I was hoping I could use CUDA to take an advantage of GPGPU but that won't happen. Anyway, thanks for all the suggesti ...
written 28 days ago by akh2230
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Forum: Bioinformatics Workstation Suggestions
... Hi We will invest some money in building a lab workstation dedicated to run bioinformatics analysis suites for RNAseq and scRNAseq, and I am curios to see what sort of configurations most use. We are looking at Dell XPS with i9 (whopping 8 cores), 64GB DDR4, NVIDIA® GeForce® GTX 1080 8GB GDDR5X an ...
forum next-gen rna-seq workstation written 4 weeks ago by akh2230 • updated 4 weeks ago by Dave Carlson90
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scRNA Cell Type ID web resources
... HI, There are literally dozens of web resources that helps you identify cell clusters generated by scRNAseq. I've uncovered and tried a few of them and there are pros and cons of each of these sites. I am curios to see which web sites are preferred or popular, and I'd appreciate if I can get a f ...
next-gen rna-seq scrnaseq written 4 weeks ago by akh2230 • updated 4 weeks ago by jared.andrews072.7k
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Answer: A: Why does Rsubread featureCounts with Ensemble GRCm38.96.GTF picks ensembl_exon_i
... I sort of figured this out. I had run the same script in.another of my Macmini running Mojave and exactly the same versions of Rstudio and R (bioconductor packages) and worked as expected. I noticed Rstudio was acting wacky so I deleted and reinstalled Rstudio and after that, the featureCount s ...
written 5 weeks ago by akh2230
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Comment: C: Why does Rsubread featureCounts with Ensemble GRCm38.96.GTF picks ensembl_exon_i
... here we go; $counts Skin.25.IT.1.21.19.bam Skin.26.IT.1.21.19.bam Skin.27.IT.1.21.19.bam Skin.28.IT.1.21.19.bam Skin.29.IT.1.21.19.bam ENSMUSE00001343744 0 0 0 0 0 ...
written 5 weeks ago by akh2230 • updated 5 weeks ago by h.mon26k

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Popular Question 4.5 years ago, created a question with more than 1,000 views. For A strategy to get Bacterial NCBI RefSeqs excluding contigs in an one file

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