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Recent Replies
Comment: Getting the overlap between two GTF files
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GenoMax
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Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
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Pierre Lindenbaum
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> My problem has been with trying to loop the process.
ok here is a **nextflow** based solution,(NOT tested)
workflow {
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I see.
I tried using the GUI Rockhopper for RNA-seq analysis of a K. pneumoniae strain, but the program didn't find the strain's assembly…
Answer: Getting the overlap between two GTF files
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Pierre Lindenbaum
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bedtools intersect \
-a <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf | sort -t $'\t' -k1,1 -k2…
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I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.
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There is no package of that name in CRAN or Bioconductor. Where do you have it from, so which tutorial you follow?
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thank you. This is exactly what I was looking for
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This is not the most elegant solution, but it should work with previous suggestions.
In this remote directory:
http://ftp.wwpdb.org/p…
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The manual says you can split samples out at once using the `+split` plugin. So, `bcftools +split -Oz -o <PATH> file.vcf.gz` should do the …
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Phate (or Monocle) doesn't do UMAP. If you have done UMAP already (using seurat) then you could use the cell barcode to UMAP cluster label …
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I figured out how to make it work. The bams have to be comma separated not just by space:
cd "${input_directory_with_associated_bam_fi…
Comment: Search RCSB with a list of protein names?
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Joseph
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Hey, this is so close to what I'm looking for - I clarified in my edit. This is a great way to batch download lots of PDBs in RCSB by their…
Comment: Search RCSB with a list of protein names?
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Joseph
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This is a really neat package, but I don't think it does exactly what I want, so I've clarified my question. This seems like it grabs a PD…
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Chris
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Yes, thank you! I figured it out but I got an error:
velocyto run10x -m Hg38_rmsk.gtf WT/outs /cellranger/reference/refdata-cellranger…
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You can get from here- [UCSC][1]. Just click on get output botton.
[1]: https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=611454127_NtvlaW…
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