Counting 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...
View ArticleExtract rows from BED file on the base of text content in one column
Hi,I am a newbie with scripting so I can't find an easy solution to this question by myself and I'd like to ask for some help.I have a long list of BED files, and for each file I want to scan them row...
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 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 ArticleProblem With Counting Mapped Reads
Hi, This is my very first experience analysing RNAseq data. My goal is to do differential analysis between two strains of a bacteria. So far, i managed to align and produce SAM and BAM files. I'm...
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 ArticleBedtools intersect tab and bed files
How can you call Bedtools intersect on a tab and bed file? without getting the typical:"Differing number of BED fields encountered at line: #. Exiting..."Error.My bed file has 15 columns and my tab...
View ArticleHow To Get Fasta Format Using Fastafrombed Or How To Turn Linearized Fasta To...
I extracted sequences with fastaFromBed and have no complains about the BEDTools which is really awesome thing.Otherwise extracted sequences look like this:>chr19:13985513-13985622...
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 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 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 ArticleExtract coverage per feature from a bam and bed to a file
Hi, a simple task.. or should be. I need to extract the average coverage per feature in a bam file. I have a genbank and bed file for the reference the bam was mapped to. if I map with e.g. Geneous...
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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 ArticleBedtools on Cygwin problem.
Hi I'm trying to install the latest release of Bedtools via Cygwin but there's a weird error during process. I know this isn't the best solution, but I do not have an other choice. Perhaps anyone...
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 ArticleN Closest Genes To A Given Location
Hi,This is basically an extension of the following question already asked in biostar (http://biostars.org/post/show/53561/python-finding-gene-closest-to-a-given-location/).Let us say I have a list of...
View ArticleCoveragebed, Depth/Breadth Of Coverage
I'm using coverageBed to calculate the depth and breadth of coverage, but I'm not sure I'm doing this right. I want to calculate the two values for each human chromosome. For example, I've created a...
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How To Explain Uneven Coverage Of A Dna Seqment Obtained Via Pcr Amplification.
Experiment: deep sequencing for mutants in 700nt fragment.the fragment of dna was preamplified by primers flanking the fragment followed by hiseq.per base coverage was calculated by coverageBed -d...
View Articlebedtools 2.0 merge - "unable to open file or unable to determine types"
I have a sorted bedfile comprised of three columns: seqid, start, and end. sort -k1,1 -k2,2n tmp2.bed > tmp3.bed 1 6589256 6589207 1 11627195 12127194 1 12616616 12116617 1...
View ArticleHeatmap Of Read Coverage Around Tsss
I am trying to plot a heatmap of read density around a feature of interest (TSSs) very common in genomics papers. something like this (B): However, I am struggling a bit in getting to look "right". A...
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