User: shg018

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shg0180
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Posts by shg018

<prev • 14 results • page 1 of 2 • next >
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Single-cell RNA seq
... HI I've been trying to learn single-cell sequencing protocol from a published paper "Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer", Woosung Chung et al. 2017. The paper states that "To assess the expression values of array control RNA spike-ins ...
sequencing written 2 days ago by shg0180 • updated 2 days ago by seidel6.2k
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Comment: C: Heatmap Usage - How to color cells based on row/column names after generating ge
... It looks like th link doesn't show up for the image. Please find it below: https://ibb.co/kfNkya ...
written 14 days ago by shg0180
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Heatmap Usage - How to color cells based on row/column names after generating generic heatmap
... Hello everyone I had a question regarding possible ways of formatting heat maps. So I have a heat map like the one below, and I want to specifically highlight some cells with another color based on the name of that column. I can't find a way to do so since all I have found so far is addition of ann ...
R written 14 days ago by shg0180 • updated 13 days ago by shoujun.gu210
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SCDE Package scde.error.models ERROR
... Hi everyone I have been trying to use scde package for single cell differential analysis and I have been getting an error on using: o.ifm <- scde.error.models(counts = cd, groups = sg, n.cores = 10, threshold.segmentation = TRUE, save.crossfit.plots = FALSE, save.model.plots = FALSE, verbose = ...
single-cell R rna-seq written 9 weeks ago by shg0180 • updated 7 weeks ago by dfscruz0
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Comment: C: SCDE Package error
... Thank you soo much!! That worked! If you don't mind me asking, when I run: o.ifm <- scde.error.models(counts = cd, groups = sg, n.cores = 10, threshold.segmentation = TRUE, save.crossfit.plots = FALSE, save.model.plots = FALSE, verbose = 1) I am getting the error that arguments must have same ...
written 9 weeks ago by shg0180
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SCDE Package error
... Hi everyone So I had a question about the scde package in R which I am trying to use for single cell analysis. When I try to run it in R using the code below: source("https://bioconductor.org/biocLite.R") biocLite("scde") I get warning message: package 'scde' is not available (for R version 3.2.3) ...
R rna-seq written 9 weeks ago by shg0180 • updated 9 weeks ago by erictleung90
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Cufflinks seg fault
... Hey everyone So I've been trying to generate read counts from my sam files. So far I have converted the sam file to bam or sorted bam and tried using the line: /opt/biotools/cufflinks/bin/cufflinks -G /oasis/tscc/scratch/shagupta/L2AnnotatedGenome.02/gencode.vM10.long_noncoding_RNAs.gtf -o transcri ...
sequencing written 5 months ago by shg0180 • updated 5 months ago by Pierre Lindenbaum98k
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Build Ensembl genome index specific to long non coding RNA
... Can someone suggest a good site to get the gtf and fasta file format specific to long non coding RNA. I used http://www.gencodegenes.org/mouse_releases/current.html and its giving me errors in calculating reads with my raw read-files after mapping with the genome built using the files at this site. ...
genome rna-seq written 8 months ago by shg0180
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Comment: C: FeatureCounts Assertion `l_name < 100' failed.
... Hi, sorry to keep bugging you, but what exactly do I look for in IGV? Also, I used my gtf and fa files from http://www.gencodegenes.org/mouse_releases/current.html since I needed specific ones for lon-non coding rna's, and I don't observe this problem when I map to a complete genome! Would you rec ...
written 10 months ago by shg0180
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Comment: C: FeatureCounts Assertion `l_name < 100' failed.
... But if I mapped using the same gtf file, that is I included the annotation file while building the genome, then how would my BAM/ SAM(in this case), have different names? Shouldn't it be continuous across all the files? ...
written 11 months ago by shg0180

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