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Bedtools Intersect related

bedtools chip-seq tool bedfiles written 10 months ago by chaudharyc61 • 20 • updated 10 months ago by 2nelly • 180

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671

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Compare a long list of BEDFiles against a whole genome/ chromosome ?

wholegenome bedfiles biopython compare written 3.8 years ago by dearbbhyc • 0 • updated 3.8 years ago by Alex Reynolds ♦ 30k

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How to create Hi-C analysis package HiFive fend object

hi-c hifive python hicup bedfiles written 4.7 years ago by jacel • 0 • updated 4.6 years ago by Biostar ♦♦ 20

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3.1k

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Does multiIntersectBed works with -u and -f parameter?

bedtools intersect bedfiles sequencing written 5.3 years ago by ivivek_ngs • 4.9k • updated 5.3 years ago by Aaronquinlan ♦ 11k

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Recent Replies

A: SSU-align running error by Naomifu • 0
Hi, did you manage to solve this problem? Thank you
C: Automatically change N for consensus sequence by cpad0112 ♦ 13k
can you please rephrase the question or give an example?
C: Automatically change N for consensus sequence by dasilvauirajan • 20
It is nucleotide sequences by the way
C: Unable to locate libraries in latest version of R 4.0.0 by cpad0112 ♦ 13k
Are you using system libraries or personal libraries? Check if new version is pushing libraries t...
A: Merged vs. Ensembl GTF for htseq-count by kristoffer.vittingseerup • 3.2k
I've written a bit about such considerations [here][1] - hope this is helpfull. [1]: https://...
A: what should I do first: transciptome annotation or DE analysis? by kristoffer.vittingseerup • 3.2k
You definitively should remove contaminants before doing your DE analysis. Else you are just test...
C: clinical trait file by parinv • 0
From one dataset I obtained information about drugs and concentration they used and age, while th...
C: SVA : Setting up the data from an ExpressionSet and applying sva function to ext by wwyue127 • 10
Hi @ivivek_ngs, Excuse me, I have two questions. 1. When you write "plPCA(co)", but I can't se...
C: Get nonoverlapping regions of two bed files by Alex Reynolds ♦ 30k
$ bedops --partition <(sort-bed A.bed) <(sort-bed B.bed) | bedops --not-element-of 1 - ...
C: Is BLAST highly sensitive? by fishgolden • 420
> So is this totally normal? Yes. Searching similar nucleotide sequences are really difficul...
C: Error while using ComplexHeatmap by mohammedtoufiq91 • 110
@Kevin Blighe , thank you so much. The issue has been resolved after upgrading both R and Complex...
A: How to use output of PANTHER Enrichment Test as input to cytoscape by kousi31 • 10
I tried http://www.pantherdb.org/ --> Statistical enrichment test. Export options for result...

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