User: from the mountains

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Posts by from the mountains

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Answer: A: How to get real cell names from Seurat Object?
... Do you mean cell type, rather than cell name? Seurat doesn't automatically annotate your cells with the cell type. You can do that through manual intervention with the `RenameIdents` function, or you can get the `SingleR` package from bioconductor to "guess" it for you. you can get the current ident ...
written 10 days ago by from the mountains130
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Comment: C: Qualimap out of memory
... I don't usually use qualimap on rna data but 1.2 Gb is usually insufficient for my exome bams, regardless of the amount of available memory. ...
written 6 weeks ago by from the mountains130
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Comment: C: Convert VCF4.1 to VCF4.2 using bcftools (preferrably)
... doesn't this do exactly that in vcftools? https://github.com/vcftools/vcftools/blob/master/src/perl/vcf-convert ...
written 7 weeks ago by from the mountains130
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ReadsPipelineSpark marking duplicates differently than MarkDuplicates
... I am using GATK 4.1.0.0 to mark duplicates in and recalibrate my bam. My workflow is currently to use: 1. MarkDuplicates 2. BaseRecalibrator 3. ApplyBQSR But recently I have wanted to replace them with spark enabled pipelines to increase efficiency. I came across ReadsPipelineSpark, which marks dup ...
gatk dna-seq alignment written 12 weeks ago by from the mountains130
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Comment: C: looking for tools to detect RNA contamination in DNA
... wouldn't you want to know if RNase treatment even worked, even if your provider says they performed it? ...
written 6 months ago by from the mountains130
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Comment: C: looking for tools to detect RNA contamination in DNA
... not sure how my previous reply didn't show up so maybe i'm double-posting. I would think you would see a lot of breakpoints coinciding with known splice sites, and maybe there's a statistical test to see if there's a preference for breakpoints at splice sites. any splice event in DNA data could be r ...
written 6 months ago by from the mountains130
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looking for tools to detect RNA contamination in DNA
... I am looking for any bioinformatics tool that might detect RNA contamination in DNA data (specifically exome data). Although RNA contamination is rare it's something we'd like to study on our samples nonetheless. Edit: some ideas: - check for rRNA contamination, something like Picard's `Collect ...
dna-seq qc contamination rna-seq written 6 months ago by from the mountains130
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Comment: C: Extract out lines with 's__' into a new file together with first two lines of th
... i've edited my comment for clarity. ...
written 7 months ago by from the mountains130
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requirements for qualimap gff file
... I am attempting to use the `qualimap bamqc` tool to get qc information and having a bit of trouble using it for testing of small inputs. I am running the following qualimap bamqc -bam smalldata.bam -c -gd HUMAN -gff newbed.bed -outdir outfolder Both the bam and the bed file are "small". i thi ...
exome qc written 7 months ago by from the mountains130 • updated 7 months ago by Ram32k
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Comment: C: Extract out lines with 's__' into a new file together with first two lines of th
... i'd add to that and say ``` grep "^#SampleID\|^ID\|s__" > extracted_file.txt ``` to make sure all matches are at the beginning of the line. you can also use option `-P` so you don't have to escape the `|` operator ...
written 7 months ago by from the mountains130

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Popular Question 7 months ago, created a question with more than 1,000 views. For bowtie issues: unable to map significant amount of pairs
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Great Question 11 months ago, created a question with more than 5,000 views. For How is Tophat installed?
Popular Question 12 months ago, created a question with more than 1,000 views. For bowtie issues: unable to map significant amount of pairs
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