Bed File Bedpe Format
Hi,I'm having trouble with converting the bam file into bed -bedpe using the bedtools.workflow: samtools sort -n mut.bam mut.Namesorted bamTobed -i mut.Namesorted.bam -bedpe >...
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 ArticleCoveragebed, Depth/Breadth Of Coverage
I'm using coverageBed to calculate the depth and breadth of coverage, but I'm not sure I'm doing this right. I want to calculate the two values for each human chromosome. For example, I've created a...
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...
View ArticleHow To Install Bedtools In A User Directory
I am trying to install Bedtools in a user directory, however I looked at the manual for its makefile, and there is no such argument like "--prefix" for me to change. Is there a way to install all...
View ArticleProblems Extracting Non-Snps From A Vcf File
Hello,In an SNP analysis, I am trying to extract those editing sites no found in the dbSNPs vcf file I have downloaded a couple of files (All SNPs and Common/Medical SNPs) from...
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 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 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 ArticleDiscrepancy In Samtools Mpileup/Depth And Bedtools Genomecoveragebed Counts
I am getting different counts for the number of bases on reference covered by aligned reads using samtools depth/mpileup and BEDTools genomeCoverageBed commands. I am using samtools-0.1.19 and...
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 ArticleQuestion about number of reads within intervals
Hi there, This question is very basic but I need to ensure that I'm going on the right way. I need to calculate the number of reads falling inside my bed intervals and the number of reads falling...
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 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 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 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 "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 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 ArticleSplice Junction file intersection with genome annotation
Hello, I have a tab delimited format Splice Junction file and the file looks something like this: chr1 11212 12009 1 1 0 0 2 48 chr1 11672 12009 1 1 0 0 1...
View ArticleExtract rows from BED file on the base of text content in one column
Hi,I am a newbie with scripting so I can't find an easy solution to this question by myself and I'd like to ask for some help.I have a long list of BED files, and for each file I want to scan them row...
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