User: shg018

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shg0180
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Posts by shg018

<prev • 11 results • page 1 of 2 • next >
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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 11 days ago by shg0180
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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 11 days 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 11 days ago by shg0180 • updated 11 days 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 3 months ago by shg0180 • updated 3 months ago by Pierre Lindenbaum96k
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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 7 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 8 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 9 months ago by shg0180
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Comment: C: FeatureCounts Assertion `l_name < 100' failed.
... So, I used htseq-counts to read counts this time, using the sam files this time, and I get a file with 0 reads: __no_feature 1358293 __ambiguous 0 __too_low_aQual 0 __not_aligned 0 __alignment_not_unique 2714159 and a warning during runtime: Warning: Mate records missing f ...
written 9 months ago by shg0180 • updated 9 months ago by Devon Ryan69k
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Comment: C: FeatureCounts Assertion `l_name < 100' failed.
... Would you recommend any way of fixing this, without going and manually editing gene name in the annotation file? ...
written 10 months ago by shg0180
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Comment: C: FeatureCounts Assertion `l_name < 100' failed.
... Thanks!! This really helped! :) ...
written 10 months ago by shg0180

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