Bedtools "Segmentation Fault" While Working With Genome.Fa
I wanted to use BEDTools to extract genomic sequences (fastaFromBed). My BED file has all 24 chromosomes, hence I want to use whole genome (merged from chromosome.fa). Tried to: fastaFromBed -fi...
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 ArticleBed File Bedpe Format
Hi,I'm having trouble with converting the bam file into bed -bedpe using the bedtools.workflow: samtools sort -n mut.bam mut.Namesorted bamTobed -i mut.Namesorted.bam -bedpe >...
View ArticleGiven gene ID and genomic coordinates, how can I create a GFF formatted file?
 I have downloaded a list of coordinates of yeast genes from Xu et al., 2009 (see table S3). Unfortunately its current format is not a standard format so it does not appear to be compatible with the...
View ArticleFinding Overlapping Variants (I.E. Indels, Snps) Using Annovar Format.
Hello,I know that using bedtools functions (specifically intersect and windows), it is possible to find overlapping features in the two sets of data. The catch here is that bedtools only accept the...
View ArticleHow To Find The Nearest Gene To A Retrotransposon Insert?
Hi,I have a BED file with the position of retrotransposons in the mouse genome and I would like to find the nearest gene, the distance to that gene and whether it is on the + or - strand. There are so...
View ArticleGet The Idea Of Splicing From Reads Mapped In Rna-Seq
I've got a set of 100 bam files from a public experiment, I want to have an idea of splicing in each of them regarding three exons,without entering in some kind of depth-level procedure like Cufflinks...
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Profile Coverage Of Rnaseq Samples?
Hi all,I have a quick question:How can I visualize aligned paired-end reads from RNAseq datasets in UCSC browser?I already mapped the reads and assembled the transcripts with Tophat/Cufflinks but I'm...
View ArticleBed File Of Mapq Sliding Window On A Bam File?
There may already be a recipe for this, so asking first before reinventing the wheel: I would like to create a bed file where the score is the average mapQ from the reads of the input.bam file. I think...
View ArticleDoes Windowbed Extend Reads?
I am using WindowBed, part of the BedTools suite, to align reads to a reference file and I obtained a very interesting result. I am trying to rule out an analysis artifact that could be caused by...
View ArticleIntersect Gene Annotation With Specific Position Or Genomic Interval
Hi,I've several genomic interval and I want to check if they are overlapping with known gene. I've a gtf file with the coordinates of gene exons. My idea was to use intersectBed from bedtools but I've...
View ArticleIntersectbed Tool Generating Empty File
I have used the Bedtools command intersectBed to check the overlap between two bed files. A is my INDEL file and B is my Reference file. But it is producing an empty output file. I thought the problem...
View ArticleMulti Thread Bedtools
Hi,Is there a multi thread version of bedtools ? or is this feature in development ? Thanks,N.
View ArticleTool: Bedtools: Analyzing Genomic Features
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 representation and query is...
View ArticleDetermining Each Samples Coverage Area
First time I am working with NGS data. I've got a BAM file with mapped reads for my samples and a BED file with the regions in HG19 that were targeted (used an Ion-torrent ampliseq panel). Are there...
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Extract Only Paired-End Reads That Map A Specific Interval
Hi,Is it possible to extract paired-end reads that map to a specific interval ( from a bam file ). I tried with intersectBed :intersectBed -abam align.bam -b interval.gff3 -wa > result.bamhere's the...
View ArticleTutorial: Piping With Samtools, Bwa And Bedtools
In this tutorial I will introduce some concepts related to unix piping. Piping is a very useful feature to avoid creation of intermediate use once files. It is assumed that bedtools, samtools, and bwa...
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 ArticleBedtools Multicov Need A Bam Index File Specification Option
bedtools version 2.16.2 multicov used to compute the multiple sample coverage given a feature file(gtf bed).format: bedtools multicov -bams alin1.bam aln2.bam .. -bed capturRegion.bed...
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...
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