Bedtools 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 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 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 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 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 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 ArticleGTF2/GFF3 "feature" types and expression analysis
Hi, I aligned a few samples using STAR to the genome provided in the Illumina iGenomes UCSC hg19 bundle (here) -- I used the provided gene feature (gtf2) file as is. Now, my motive is to calculate the...
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: 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 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 Overlap
Hi,I've a question about intersectBed. Is it possible to extract only alignment like this :chromosome =============================================================== BED/BAM A ==============...
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 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 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 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 ArticleHow Do You Get The Quality Score And Coverage For Every Single Position Of A...
Hi,I am trying to extract the coverage and the average quality score for each position of a reference assembly in bam/sam format. I have managed to get the coverage using BEDtools genomeCoverageBed...
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 Articlecompute normal-tumor coverage ratio from exome BAMs
Could someone please suggest a quick way to compute the data ratio of uniquely mapped reads in the normal to uniquely mapped reads in the tumor, as required by Varscan in the command below? I have over...
View ArticleHow To Use Bedtools To Extract Promoters From A Mouse Bed File
Hello, I would like to know how to use Bedtools to extract promoter sequences (as FASTAs) from the mouse genome (mm9) starting from a BED file.
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...
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