Bedtools Genomecoveragebed Usage : How To Create A Genome File?
I am using BEDTOOLS and the following command to get the coverage file:$ ./genomeCoverageBed -ibam ~/GG_project/trim/ecoli.bam -g > ~/GG_project/trim/coveragewhere ecoli.bam is my sorted bam file,...
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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 ArticleConvert .Txt Into Bed Files
I used paired-end sequence data for copy number variation study; and eventually get .txt files as output. I'm hoping to use Bedtools to compare my results with others. Can I convert .txt files into...
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 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 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 ArticleIntersectbed Overlap
Hi,I've a question about intersectBed. Is it possible to extract only alignment like this :chromosome =============================================================== BED/BAM A ==============...
View ArticleCounting The Whole Insert Size From Paired-End Reads As Coverage
We have updated our workflows for per base sequence coverage to use genomeCoverageBed from BAM files. However for pair-end data it seems as though the regions between pair-end reads are not counted. To...
View ArticleConverting Gff To Bed With Bedtools?
I use bedtools's sortBed utility to sort BED files for various operations. It takes as input GFF files as well. However, when I feed it a GFF file as in:sortBed -i myfile.gffit outputs it as GFF, not...
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 ArticleGetting The Average Coverage From The Coverage Counts At Each Depth.
Hi, I have read quite a few posts here about coverage already. But I still had a few questions. I have a BAM file I'm trying to find the coverage of it (typically like say 30X). So, I decided to use...
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 ArticleDoes Bedtools Intersect -V Consider Unmapped Reads "As Not In B"
bedtools intersect -v -abam my.bam -b myregions.gff > notinmyregions.bamwould we see reads with 4 in the FLAG field - i.e. unmapped reads in notinmyregions.bam
View ArticleHow To Extract Scores From Bedgraph File Using Bed Tools
file1chr1 10 20 name 0 +file2chr1 12 14 2.5 chr1 14 15 0.5How could i extract average scores of file1 using file2, like below? I am trying to extract phastcons (file2) average scores of file1.chr1 10...
View ArticleHow Can I Compare And Merge Bed Files
I have three bed files with chrNo, start, end position and type. I need to compare each chrNo, start and end position of one file with 2 other files and write the common one in a new file. Can any one...
View Articleerror with bedtools slop
Hi, I am trying to run a bedtools slop on my.bed file and hg19.genomebedtools slop -i H3K27me3.bed -g hg19.genome -b 30I get the following error:Less than the req'd two fields were encountered in the...
View ArticleSamtools or Bedtools: How to filter a bam file with a bed file using strand...
HiI would like to filter a bam file, keeping only reads overlapping with genomic intervals from a bed file. I used samtools for this:samtools view -b -h -L bedfile.bed bamfile.bam However the -L option...
View ArticleHow To Create A Read Density Profile Within A Interval?
HI!I need some help: I have to create density profile with a window specific of 1kb (how many time a sequence is detected after NGS method). I have to use SAM and BEDtools, I think I can use genomeCov...
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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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...
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