error 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 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 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 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 Articlemacs and bedtools
HelloI have MACS2 output and now looking for peaks which are situated in introns. I have bed file with introns from USCS for my species. What file with peaks should I use for bedtools intersection?...
View ArticleReproduce Encode/Cshl Long Rna-Seq Data Visualization Viewed In Ucsc, But...
Motivation The ENCODE data comes out, and luckily they provide both .bam file and .bigwig file. Thus, it occurs to me that I want to give a try to reproduce the data visualization with tool: BEDtools...
View ArticleCreating Bed File For Lncrna Using Gencode Gtf File
Hi all,I want to get the bed file of lncRNA based on GENCODE GTF fileI download the file "gencode.v16.long_noncoding_RNAs.gtf.gz", and extract the chr, start, end info from the file, then I use...
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 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 ArticleIs It Possible To Filter Only Bookend Reads From A Bed File?
I have a bed file with many fragments, some overlapping, some on their own and some adjacent to each other (book-ended) features.I know can group overlapping and book-ended features using bedtools...
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 ArticleConvert Bamtobed Score
Hey,just a short question....is there a possibility to set the score in the bed file to "1" an not to the the alignment score?? arguments -tag and -ed only use BAM alignment tags... ?!? :/Cheers!
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 ArticleIdentify Overlapping And Non Overlapping Regions For Paired-End Data
gene1 gene2 chr1 25 30 chr1 34 37 chr1 15 20 chr1 25 28 chr1 80 90 chr1 10 13 gene1 gene2 chr1 25 30 chr1 36 39 chr1 15 20 chr1 18 20 chr1 80 90 chr1 19 22 common gene1 uniq gene2 (when we compare file...
View ArticleRandom shuffling of features leaving gene models intact
I am looking for a tool that can randomly shuffle gff features into intergenic regions, but leaving the gene-models 'intact', so that at least all features of a gene are placed on the same contig and...
View ArticleIntersectbed Overlap
Hi,I've a question about intersectBed. Is it possible to extract only alignment like this :chromosome =============================================================== BED/BAM A ==============...
View ArticleDifferent coverage from bedtools and in vcf file - HELP PLEASE
Dear all, I have trouble to understand how bedtools computing coverage. I have vcf file (generated from Illumina somatic caller) - I was created bed file from my vcf. Then I try to compute coverag with...
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 ArticleWhich Of The Genes Are Enriched With Repeat Elements
I would like to know which of my genes are enriched with repeats of LINE/SINE/ERV etc. elements. I have a bam file and the repeats in bed format. As far as I know BAM files contains aligned data for...
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,...
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