Multi Thread Bedtools
Hi,Is there a multi thread version of bedtools ? or is this feature in development ? Thanks,N.
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 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 ArticleDetermining Each Samples Coverage Area
First time I am working with NGS data. I've got a BAM file with mapped reads for my samples and a BED file with the regions in HG19 that were targeted (used an Ion-torrent ampliseq panel). Are there...
View ArticleBedtools 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,...
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 ArticleChanging Column Order In Bed File
Here is my data with A, B, C and D columns in my bed file. A. B. C. D. Chr 1. 1. 12. + Chr 2. 24. 56. +How can I move my D column to position 1 where the Column A right now?
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 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 ArticleGet The Idea Of Splicing From Reads Mapped In Rna-Seq
I've got a set of 100 bam files from a public experiment, I want to have an idea of splicing in each of them regarding three exons,without entering in some kind of depth-level procedure like Cufflinks...
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 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 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 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...
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 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 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 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 ArticleSplit A Bam File Into Several Files Containing All The Alignments For X...
Hi everyone! I am struggling with annotating a very big .bam file that was mapped using TopHat. The run was a large number of reads : ~200M. The problem is that when I now try to Annotate each read...
View ArticleBedtools To Compare A Vcf File From Samtools Mpileup With Dbsnp?
Hello,I have one big vcf file which is genereated by samtools mpileup by comparing 6 cell lines to see whether there are SNP differences between them.I would like to use bedtools for intersecting. How...
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