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Recent Replies
Comment: Weirdness in annotation (missing allele frequencies)
by
Jeremy Leipzig
21k
0.60625 is 97/160 so if you have 80 individuals in your VCF that's an internal allele frequency, not gnomAD
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
•
0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
Comment: Weirdness in annotation (missing allele frequencies)
by
Can Abdullah
•
0
Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
Comment: Getting the overlap between two GTF files
by
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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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> My problem has been with trying to loop the process.
ok here is a **nextflow** based solution,(NOT tested)
workflow {
…
Comment: Assessing Rockhopper's output
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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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bedtools intersect \
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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?
Comment: Subclustering of intergated cells from scRNA-seq data
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fifty_fifty
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thank you. This is exactly what I was looking for
Answer: Search RCSB with a list of protein names?
by
Mensur Dlakic
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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…
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
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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 …
Comment: differences between trajectories in conditions with Monocle3 or other tools
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Amitm
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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 …
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
by
Y
•
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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?
by
Joseph
•
0
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…
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