Intersectbed Overlap
Hi,I've a question about intersectBed. Is it possible to extract only alignment like this :chromosome =============================================================== BED/BAM A ==============...
View ArticleGetting Rna Sequences From Gff And Fa Files
Hi. I have a folder full of .fa files, and a .gff. The gff file contains information about which loci look like they code for RNA sequences. The .fa contain the DNA sequences for a set of human...
View ArticleTutorial: Introduction to bedtools.
We have created a basic tutorial introducing bedtools. It is intended for folks that are new to the tools, but in addition, there are some puzzles at the end that may be useful for people that use...
View ArticleWhy does BedTools Map operation produce all dots as output?
I am using BedTools Map operation to map the DNAse I signal of a cell type into some chromosome regions, by computing the mean on the third column The command I use is the following: $ bedtools map -a...
View Articlehow to run subtract command in java
I want to run subtract command in java, could somebody tell me how to use.Thank you very much.
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 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...
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...
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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 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 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 ArticlePicking Random Genomic Positions
I do have a set of TF binding coordinates and want to see if there is any significant overlap with an open chromatin annotation.Example of TF coord: chr1 19280 19298 chr1 245920 245938 chr2 97290 97308...
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...
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 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 Articleproblem with bedtools complement: how to extract strand information?
Hi everyone,I have a minor trouble when using bedtools complement. My gff3 file contains Chr start end strand ect. information. I want to use bedtools complement to extract other regions, however,...
View ArticleHow To Check Whole Genome With Bigwigsummary ?
Hi,I have question about bigwigsummary tools ,I have my start and end positions and my bigwig file but I want to check whole genome instead of chromosome by chromosome Is there any option to use this...
View ArticleSnps Comparison
Hello,I would like to compare SNPs from different methods:number of SNPsSNPs postion (position where method A has SNPs but not B and vice versa. Where both have SNPs)I would be interested to get a...
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 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.
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