User: kevin.stachelek

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Posts by kevin.stachelek

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Adjusting distance between chromosome ideograms in karyoplote R
... The ideogram is created by `plotKaryotype` which itself calls `kpAddCytobands` which calls `graphics::rect`. The linewidth argument `lwd` to this function was helpful for me to increase the spacing between chromosomes. It can modified at the level of `plotKaryotype` via ellipses. ...
written 4 weeks ago by kevin.stachelek10
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choice of reference genome when comparing counts of repetitive elements
... I am using [Tetranscripts][1] to identify changes in repetitive elements in exosome contents. I am concerned that the distribution and quantity of repetitive elements might be very different between reference genomes. Do you have any guidance on choosing an appropriate reference? premade gtf files a ...
genome written 4 weeks ago by kevin.stachelek10
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Comment: C: Repeat masked gtf files from ensembl
... Ah, I see. think the 'exon' annotation be a confusing shortcut; the actual annotated feature is a LINE-1 element ...
written 5 weeks ago by kevin.stachelek10
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Comment: C: Repeat masked gtf files from ensembl
... Sorry, it appears to me that these gtf files are for the gene annotation in ensembl rather than an annotation of the masked regions (types of transposable elements, repeats, etc.) Am I misunderstanding? ...
written 5 weeks ago by kevin.stachelek10
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Comment: C: Repeat masked gtf files from ensembl
... Thanks for helping me clarify. I'm looking for a gtf file containing the locations of all masked regions in the ensembl reference genome. It might look like this: chr1 hg38_rmsk exon 67108754 67109046 1892.000000 +. gene_id "L1P5"; transcript_id "L1P5"; ...
written 5 weeks ago by kevin.stachelek10 • updated 5 weeks ago by genomax78k
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Comment: C: Repeat masked gtf files from ensembl
... Hi, yes the gff (or gtf) file is what I'm looking for. Something analogous to [this file][1] from UCSC. [1]: https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=611454127_NtvlaW6xBSIRYJEBI0iRDEWisITa&clade=mammal&org=Mouse&db=mm10&hgta_group=allTracks&hgta_track=rmsk&hgta_tabl ...
written 6 weeks ago by kevin.stachelek10
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Repeat masked gtf files from ensembl
... I am looking for a repeat masked version of a reference genome from ensembl. I find information posted [here][1] that suggests accessing via [ftp][2]. I can't find figure out what subdirectory it might be hiding in. Searching via command-line didn't turn anything up. I could run repeat-masker myse ...
genome ensembl rna-seq written 6 weeks ago by kevin.stachelek10 • updated 6 weeks ago by h.mon29k
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Comment: C: Plot normalized coverage across genes/transcripts in single cell rna seq data
... thanks. I'm working with Smart-seq data so I hope I have enough reads to make an intelligible plot. ...
written 12 weeks ago by kevin.stachelek10
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Plot normalized coverage across genes/transcripts in single cell rna seq data
... I'd like to generate a plot similar to the included image. What is the name of such a plot and does there exist a simple tool to generate, preferably compatible with multiqc and/or R/bioconductor? ![enter image description here][1] [1]: https://external-content.duckduckgo.com/iu/?u=https%3A%2F% ...
R single cell rna-seq written 3 months ago by kevin.stachelek10 • updated 3 months ago by kristoffer.vittingseerup3.0k
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Comment: C: Double Check VCF Calls in Corresponding .bam Files
... I believe that any caller will only make a call at a site which differs from the reference, otherwise the file size of vcfs would be huge. Is it true that most would have built in filters for mapping quality and base quality, i.e. --min-MQ or --min-BQ for mpileup > bcftools. Just to be clear, i ...
written 5 months ago by kevin.stachelek10

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