Random shuffling of features leaving gene models intact
I am looking for a tool that can randomly shuffle gff features into intergenic regions, but leaving the gene-models 'intact', so that at least all features of a gene are placed on the same contig and...
View ArticleUsing Gnu Parallel For Bedtools
I am trying to run gnu:parallel on bedtools multicov function where the original command is bedtools multicov -bams bam1 bam2 bam3.. -bed anon.bed > Q1_Counst.bedI would like to implement the above...
View ArticleTo Group Items In Bed Files
For example, we now have a bed file:chr1 23455 45678 chr1 23446 45663 chr1 23449 45669 chr1 30000 31000Is there anyway to group the first three lines, while leaving the last line alone? I know Bedtools...
View ArticleSnps Comparison
Hello,I would like to compare SNPs from different methods:number of SNPsSNPs postion (position where method A has SNPs but not B and vice versa. Where both have SNPs)I would be interested to get a...
View ArticleSamtools or Bedtools: How to filter a bam file with a bed file using strand...
HiI would like to filter a bam file, keeping only reads overlapping with genomic intervals from a bed file. I used samtools for this:samtools view -b -h -L bedfile.bed bamfile.bam However the -L option...
View ArticleBedtools Intersectbed
Apologies if this is blatantly obvious!I would like to compare coordinates in setA with those of setB. The output should have the same number of coordinates as setA and tell me how many nucleotides of...
View Articlehow to get -nms for bedtools
I'd like to merge bed files and preserve the names of the merged features using bedtools -nms option.However, this option (-nms) is deprecated in the newer bedtools.The documentation says I can use -o...
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Converting Bam To Bedgraph For Viewing On Ucsc?
I'm trying to go from a BAM file to a representation viewable in UCSC, ideally bedGraph. I am trying to use Bedtools's genomeCoverage like this: genomeCoverageBed -ibam accepted_hits.sorted.bam -bg...
View ArticleRunning BedTools on Linux Cluster: Permission Denied
I been having some problems with running BedTools binaries in a linux cluster. I have the binaries in my own $HOME/bin file and when I try to run bedtools I get this error message -bash: bedtools:...
View ArticleGetting All Reads That Align To A Region In Compact Bed Format Using Bedtools?
I'm trying to find all the reads (by name) from a BAM file that align to various regions in a bed file. Right now I can do this with bedtools using intersectBed:intersectBed -abam reads.bam -wo -f 1 -b...
View ArticleCorrelation Of Fpkm And Length Normalized Transcript Mapped Read Count
Hello, in the process of estimating expression for a 16 human tissue dataset ("Human Body Map 2.0 GSE30611") I used different methods to estimate the expression of the genes. After mapping against hg19...
View ArticleHow To Find The Closest Distance From Bed Files Between Genes And Repeats...
How can I use the closestBed from bedtools to find the closest locations between two bed files. The important bit here is that i want them to be upstream and in correct oriantation.When I use the -s...
View ArticleTool For Binning Windowbed Output For K-Means Clustering
I have mapped high resolution ChIP-seq data to transcription start sites using windowBed. I now want to bin the data, in bin sizes of my choosing, relative to TSSs so that I can generate heat maps and...
View ArticleSplit A Bam File Into Several Files Containing All The Alignments For X...
Hi everyone! I am struggling with annotating a very big .bam file that was mapped using TopHat. The run was a large number of reads : ~200M. The problem is that when I now try to Annotate each read...
View ArticleBedtools Compare Multiple Bed Files?
I've been dealing with comparison between two bed files using intersectBed -a -b command. I'm just wondering, is there any commands in Bedtools which can help us compare multiple bed files? Say, I have...
View ArticleFastafrombed Problem
hi, I try this tools from BedTools but it doesnt work!$ cat testgenome404.fa>chr1 AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG $ cat test.bed chr1 5 10 $ ./fastaFromBed -fi testgenome404.fa -bed...
View ArticleIntersectbed Provides An Empty Output
Hi,I've downloaded the recent Cygwin version 1.7.24 and an trying to run bedTools but I get an empty file as my output. When I run the same commandline and files on a colleagues computer also through...
View ArticleComparative Snp Analysis
Hello, I am trying to compare the degree of A-to-G editing in a near-to-isogenic pair of cell lines. I have two biological replicates and have mapped with Bowtie and BWA, followed by a samtools mpileup...
View ArticleDifferent coverage from bedtools and in vcf file - HELP PLEASE
Dear all, I have trouble to understand how bedtools computing coverage. I have vcf file (generated from Illumina somatic caller) - I was created bed file from my vcf. Then I try to compute coverag with...
View ArticleDoes Bedops Have A Command Similar To The Bedtools Makewindows?
With bedtools you can make genomic windows from a genome file or a bed fileinput.bedchr1 1000000 1500000 chr3 500000 900000[prompt]$ bedtools makewindows -b input.bed -w 250000chr1 1000000 1250000 chr1...
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