Fastafrombed Problem
hi, I try this tools from BedTools but it doesnt work!$ cat testgenome404.fa>chr1 AAAAAAAACCCCCCCCCCCCCGCTACTGGGGGGGGGGGGGGGGGG $ cat test.bed chr1 5 10 $ ./fastaFromBed -fi testgenome404.fa -bed...
View ArticleDoes Bedops Have A Command Similar To The Bedtools Makewindows?
With bedtools you can make genomic windows from a genome file or a bed fileinput.bedchr1 1000000 1500000 chr3 500000 900000[prompt]$ bedtools makewindows -b input.bed -w 250000chr1 1000000 1250000 chr1...
View ArticleBedtools 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 ArticleExtract coverage per feature from a bam and bed to a file
Hi, Ā a simple task.. or should be. I need to extract the average coverage per feature in a bamĀ file. I have a genbank and bed file for the reference the bam was mapped to. if I map with e.g. Geneous...
View ArticleCan Bedtools/Bedops Used To Extract Regions Where Scores Are Higher Than A...
I have a very basic question about bedtools and bedops. Can I use these tools to filter all the regions where the score is higher (or lower) than a given value? For example, let's say that I have a BED...
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 ArticleIntersectbed - Overlap Analysis Usign Vcf And Bed Files
I am trying to do an overlap analysis between 200 danish exomes (VCF courtsey: Zev) and 10 different gene regions. I would like to know what percentage overlaps between my region of interest (in...
View ArticleGenomecoveragebed - Bedtool For Reporting Per Base Genome Coverage
Hi Everyone I would nedd some help on genomeCoverageBed tool. This tools when used for finding per base genome coverage uses an option -d. I am actually interested in finding read counts for each base...
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 ArticleGenbank to bed conversion for bedtools analysis
Hi,Ā I need to use bedtools to obtain the coverage across two bam files for comparison. However, to do this, I need a .bed file of the genome features (of the reference genome used to generate the...
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 bundleĀ (here) -- I used the provided gene feature (gtf2) file as is. Ā Now, my motive is to calculate the...
View ArticleMerging/Intersecting Different Gene Annotations - Should I Extend Coordinates?
I want to create gene data-set (as big as possible), hence I am using several gene annotations. However, genes in different annotations overlap (it's the same gene). For reducing biases I overlap...
View Articlehow to get -nms for bedtools
I'd like to merge bed files and preserve the names of the merged features using bedtools -nms option.However, this option (-nms) is deprecated in the newer bedtools.The documentation says I can use -o...
View ArticleBedtools "Segmentation Fault" While Working With Genome.Fa
I wanted to use BEDTools to extract genomic sequences (fastaFromBed). My BED file has all 24 chromosomes, hence I want to use whole genome (merged from chromosome.fa). Tried to: fastaFromBed -fi...
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...
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 messageĀ -bash: bedtools:...
View ArticleTo Calculate The Exact Total Number Of Mapped Reads In Exome Regions
Dear All, I have some questions here. I want to do some quality control analysis on my exome data that are mapped on the reference genome. I am having the input bam file for a sample which contains...
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 ArticleError In Bedtools Getfasta: Chromosome Not Found
Hi, I am triing to use BEDtools to get some sequences from genomic coordinates. But I am having an errors saying " WARNING. chromosome (chr12) was not found in the FASTA file. Skipping." for each read...
View ArticleHow Can I Include One Bed File In Another Bed File ?
Hello, I have 2 bedfiles that share some common features let's call the first file A.bed (bigger file) and the second B.bed (smaller file). I would like to have a new bed file that includes everything...
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