bedtools: 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 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 ArticleIntersectbed/Coveragebed -Split Purify Exon?
all.reads.bam file records mapped RNA-seq reads data, including:exon:exon junctionexon bodyintron bodyexon:intron junctionQ1: When calculating RPKM for given RefSeq gene including all the position...
View ArticleCounting Number Of Bam Reads Directly Within Set Of Intervals With Bedtools
how can I count the number of BAM reads falling directly within a set of intervals, given in a GFF format? Note that I do not want reads overlapping the intervals, but ones that fall directly within...
View ArticleWhat Is The Fastest Method To Determine The Number Of Positions In A Bam File...
I have two very large BAM files (high depth, human, whole genome). I have a seemingly simple question. I want to know how many positions in each are covered by at least N reads (say 20). For now I am...
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 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 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 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 ArticleRaw Counts From Cufflinks Output
Hi, I want to ask how to get the raw counts from the output of cufflinks. One way to do this is to use the fpkm.raw counts = FPKM * (length of that transcript/1000) * (# of mapped reads / 1e6)The FPKM...
View ArticleCalculating Exome Coverage
*// Edit to make the post more clear (Mapping done via Bowtie2). My problem is that when counting Exome Coverage via coverageBed gives different results than via genomeCoverageBed. So I'm not sure if...
View ArticleCounting Features In A Bed File
I have a file in the following BED formatChr1 1022071 1022105 + Chr1 1022071 1022105 + Chr1 1022072 1022106 - Chr1 1022072 1022106 - Chr1 1022072 1022106 - Chr1 1022072 1022106 -I am trying get the...
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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 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 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 ArticleTo Calculate The Exact Total Number Of Mapped Reads In Exome Regions
Dear All, I have some questions here. I want to do some quality control analysis on my exome data that are mapped on the reference genome. I am having the input bam file for a sample which contains...
View ArticleExtracting Genomic Coverage Information Across Different Samples
Hello, I have 3 bam files that i wanted to compare against each other. For example i have reference file with 10,000 sequences. I have paired end reads sequenced for 3 different samples. 1) Sample 1 is...
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 ArticleRemove Intronic Regions in .BAM
HiI have a .BAM file which contains discordantly and concordantly mapped mate-pairs. I used bedtools Pairtobed to extract the mate-pairs which both show overlap with targeted regions (Illumina target...
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...
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