Top Tweets for #bedtools
2/ we need to
1. use AI
2. normalize mistakes
3. get over error messages #bioinformatics #beginner watch full video here https://t.co/C1DMFB5kxQ #bedtools #genomics #beginner #bioinformatics
If you’re starting with #bioinformatics, I recommend reading #bedtools manual, and then manuals of all the tools Heng Li has ever written. That will cover like 50% of your future daily routine:) (exaggerating, but just a little bit)
Question: I'm using #bedtools getfasta to write a fasta from an NCBI genome fasta and gff, but the fasta produced by bedtools has all of the scaffold start positions -1 compared to the gff. End position is correct. Has anyone encountered this? #Bioinformatics @aaronquinlan
Is there a #multithreaded version of the #bedtools?
We are considering projects for our #CS #intern students.
Comments welcome!!
#Bioinformatics
The idea is to create a simple, flexible, and fast DSL for genome arithmetic a la #bedtools that allows users to quickly create custom scripts or tools for cases where bedtools doesn't have what you want.
Campaign for MultiIntersectBed to have full documentation, the tool you always wanted but could never find! #bedtools #secretmenu @aaronquinlan
@zx8754 Thanks for the suggestion! I was looking for overlaps to binned hg38. I was using #GRanges findOverlap(). #bedtools intersect was substantially faster for doing this. According to @Rbloggers data.table::foverlaps is even slower than findOverlaps ()
https://t.co/GMhY5nSCWj
I have been working on code to do a task, w #GRanges for wks. Agonizing over parallelizing and efficiency. Moved to #bedtools . Worked in a minute with one line of code. I’m not saying I have regrets bc I learned a lot. But I have regrets 🤦🏼♀️
#rstats #bashftw #Bioinformatics
Created a @SingularityApp container for #bedtools, an amazing toolkit developed by the @aaronquinlan lab. Hosted an image at @SylabsIO. As always, I hope someone finds this useful besides myself. #computationalbiology #bioinformatics https://t.co/oJFyX0D9Mn
`intersect` - no need to return the metadata!
`findOverlaps` - oh hey here’s a new data structure, without the data I want
I’m now debating calling #bedtools from R as if I’m a lunatic.
@keyboardpipette I'm most comfortable with #bedtools (I don't grok iranges), hence my increasingly odd position.
For the fans of #bedtools interested to learn #rstats @Bioconductor, @lawremi has mapped bedtools recipes to #rstats scripts. Usefull resource: https://t.co/vaPBuj06Ed
We just dropped version 2.29.0 of bedtools. It includes a couple of nice new features and important bug fixes, so I would recommend updating. More fixes and requested features to come in the 2.30 release.
#bedtools
https://t.co/ZDzJDjCe85
@aaronquinlan @brent_p I. Love. #BEDTools. The speed, the docs. It's as close to perfect as I can want and these improvements will probably make my head spin...Thank you!
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