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dukecomeback
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Recent Replies
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
GenoMax
134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
Pierre Lindenbaum
157k
> 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
by
langziv
▴
50
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
by
Pierre Lindenbaum
157k
bedtools intersect \
-a <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf | sort -t $'\t' -k1,1 -k2…
Comment: Assessing Rockhopper's output
by
shelkmike
▴
980
I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.
Comment: Unable to install HorvathMammalMethylChip40manifest packages
by
ATpoint
77k
There is no package of that name in CRAN or Bioconductor. Where do you have it from, so which tutorial you follow?
Comment: Subclustering of intergated cells from scRNA-seq data
by
fifty_fifty
▴
60
thank you. This is exactly what I was looking for
Answer: Search RCSB with a list of protein names?
by
Mensur Dlakic
★
25k
This is not the most elegant solution, but it should work with previous suggestions.
In this remote directory:
http://ftp.wwpdb.org/p…
Answer: Automate the Splitting of a VCF File by Sample (bcftools)
by
Ram
40k
The manual says you can split samples out at once using the `+split` plugin. So, `bcftools +split -Oz -o <PATH> file.vcf.gz` should do the …
Comment: differences between trajectories in conditions with Monocle3 or other tools
by
Amitm
★
2.2k
Phate (or Monocle) doesn't do UMAP. If you have done UMAP already (using seurat) then you could use the cell barcode to UMAP cluster label …
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti
by
Y
•
0
I figured out how to make it work. The bams have to be comma separated not just by space:
cd "${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…
Comment: Search RCSB with a list of protein names?
by
Joseph
•
0
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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