Which Of The Genes Are Enriched With Repeat Elements
I would like to know which of my genes are enriched with repeats of LINE/SINE/ERV etc. elements. I have a bam file and the repeats in bed format. As far as I know BAM files contains aligned data for...
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 ArticleHow To Use Bedtools Windows To Overlap Upstream For Positive Strand Strand
Hi,I am trying to use bedtools windows. It has been explained in the manual of the bedtools but I am still bit confused and thought a confirmation would be good. And I have no biological background.I...
View ArticleSimple Redirection, I/O Problem With Bedtools
Hi Guys, Just a quick question. Its more of a Bash question rather than Bioinformatics, with Bedtools in question.I mostly pipe the bedtools I/O. Here's a general scenario :sed 1d fileA.bed |...
View Articlebedtools: extracting no coverage regions
Hello,I am not sure if this has been answered before as I looked and couldn't find a simple answer.I have a bam file, and all I want is to annotated all regions with 0 coverage in bed format. Is that...
View ArticleGeneral Considerations For Genomic Overlaps?
Hello I was wondering about general considerations for performing overlap of genomic regions and doing Monte Carlo-type statistics. Below I have made a description of how I do it, unfortunately Im not...
View Article"mask" values in a bedgraph
I am trying to plot average conservation in a list of genomic features, and so far managed to do it successfully using a combination of the phastCons bigwig files (hg19.100way.phastCons.bw) and...
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 ArticleBedtools "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 ArticleReporting The Bam Reads Overlapping A Set Of Intervals With Bedtools
I am trying to use bedtools to pull out the reads falling directly within a set of BED coordinates. While this command does it successfully:intersectBed -abam mybam.bam -b intervals.gff -wa -wb -f 1 |...
View ArticleIntersectbed - Overlap Analysis Usign Vcf And Bed Files
I am trying to do an overlap analysis between 200 danish exomes (VCF courtsey: Zev) and 10 different gene regions. I would like to know what percentage overlaps between my region of interest (in...
View ArticleBowtie2 Mapping Different Number Of Reads To Same Sequence When Ref-Seq Is...
I am using bowtie2 to map my PE reads. I have indexed multiple bacterial genomes by putting them together in a multi-fasta file fashion.bowtie2 -q -a -p 1 -x Multi -1 R100_1.fq -2 R100_2.fq -U...
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 ArticleIntersectbed: Return Reads In Fraction In Input Files
I have a question with respect to intersectBED and multiple input files:Is it possible to return reads which are present in, say 8/10 input files, without fractioning the reads in smaller...
View ArticleHow To Combine Fpkm Values From Cufflinks With Contigs From De Novo Assembly...
Hi all,I am working on RNA-seq data analysis. I've finished running Tophat and Cufflinks to get FPKM values for each read from Illumina pair-end sequence. Also, parallely I've run Velvet to get contig...
View ArticleDiscrepancy In Samtools Mpileup/Depth And Bedtools Genomecoveragebed Counts
I am getting different counts for the number of bases on reference covered by aligned reads using samtools depth/mpileup and BEDTools genomeCoverageBed commands. I am using samtools-0.1.19 and...
View ArticleHow To Count Genes In Genomic Regions Using A Gtf/Gff3 And A Bed File Of Regions
I'd like to count the number of unique genes in a gff file falling within a list of genomic regions. With bedtools I can count the number of regions within the gff which is almost what I want, but not...
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...
View ArticlePer Base Coverage
Is there a way to obtain per-base coverage for a define chromosome interval using a bam file generated from Illumina single-end reads? genomeCoverageBed in Bedtools does not seem to have an option for it.
View ArticleHelp With Exception When Using Bedtools Coveragebed With Paired Alignment....
I use bwa mem to align paired reads to few hundreds of microbial contigs; then I sort the alignment, and trying to get a coverage using bedtools genomecov -ibam alignments.paired.sorted.bam -bg...
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