Get Complement Of Two Bed Files

I would like to get the complement of a bed file Answer: Use: [http://code.google.com/p/bedtools/][1]

Returns all intervals not spanned by the features in a BED/GFF/VCF file.

bed next-gen sequencing sequencing file

• 238 views • link

updated 16.0 years ago by Neilfws 4.9K • | written 16.0 years ago by D W 15

please delete this post

• 0 views • link

written 16.0 years ago by D W 15

as you wish :-)

• 0 views • link

written 16.0 years ago by Neilfws 4.9K

0 answers

No answers yet.

More posts like this

Bed file coordinates
written 5.7 years ago by storm1907 3

Hello, I am supposed to extend bed file coordinates by 2bp with Bedtools. I am very new to field and have a poor understanding about …
Bedtools intersect behavior under different coordinate systems?
written 8.1 years ago by edsouza 3

I'm currently waiting for a pipeline I'm running to produce some BED files and VCF files, which I will then intersect with a GFF file …
coordinate of BAM and BED
written 8.9 years ago by yuabrahamliu 6

Hi all, I want to use `bedtools multicov` to count the RNAseq reads in specific bed file intervals (containing all the intron intervals of mm10 …
Tutorial: InsideDNA: How to use BEDTools for analysis of genome methylation
written 10.2 years ago by shilparaopradeep 19

BEDTools is an extensive suite of utilities for genomic features analysis. There are several common genomic file formats, such as: BAM, GFF, GTF, VCF and …
Bedtools coverage adding feature scores
written 10.3 years ago by jaime alvarez 3

I am trying to calculate the coverage of features in a gff file and a bed file containing the windows. The bed file (windows_test.bed), note …
per bp depth intersected with gff file
written 11.5 years ago by Biomonika (Noolean) 323

Hi all, I have a bam file and gff file and need to report per base coverage for all intervals (features) from gff file. Instead …
Finding Overlapping Variants (I.E. Indels, Snps) Using Annovar Format.
written 12.6 years ago by youngcsong 10

Hello, I know that using <a href='https://code.google.com/p/bedtools/'>bedtools</a> functions (specifically intersect and windows), it is possible to find overlapping features in the two sets of data. …
How Can I Include One Bed File In Another Bed File ?
written 13.1 years ago by fmfshog 0

Hello, I have 2 bedfiles that share some common features let's call the first file A.bed (bigger file) and the second B.bed (smaller file). I …
Converting Gff To Bed With Bedtools?
written 13.7 years ago by user 96

I use [bedtools][1]'s `sortBed` utility to sort BED files for various operations. It takes as input GFF files as well. However, when I feed it …
Tool: Bedtools: Analyzing Genomic Features
written 14.4 years ago by Istvan Albert 10K

All practicing bioinformaticians will face problems that require them to compare, query and select genomic features across an entire genome. As it happens efficient interval …