Bedtools Multicov Need A Bam Index File Specification Option
bedtools version 2.16.2 multicov used to compute the multiple sample coverage given a feature file(gtf bed).format: bedtools multicov -bams alin1.bam aln2.bam .. -bed capturRegion.bed...
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 ArticleGetting Unmapped Reads: Comparing Fastq To Bam
given a FASTQ file and a BAM file of aligned reads, is there an efficient way to get all FASTQ reads that are in the original FASTQ but not in the BAM? Perhaps using bedtools. i.e.:unmapped_script...
View ArticleWhat Is The Fastest Method To Determine The Number Of Positions In A Bam File...
I have two very large BAM files (high depth, human, whole genome). I have a seemingly simple question. I want to know how many positions in each are covered by at least N reads (say 20). For now I am...
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 ArticleCounting The Whole Insert Size From Paired-End Reads As Coverage
We have updated our workflows for per base sequence coverage to use genomeCoverageBed from BAM files. However for pair-end data it seems as though the regions between pair-end reads are not counted. To...
View ArticleSimple Redirection, I/O Problem With Bedtools
Hi Guys, Just a quick question. Its more of a Bash question rather than Bioinformatics, with Bedtools in question.I mostly pipe the bedtools I/O. Here's a general scenario :sed 1d fileA.bed |...
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 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 Can I Merge Intervals ?
Hello everybody, I should be grateful if you would kindly help me de fix my problem. I have a table like that :Chromosome start end info1 info2 chr01 1 100 15 35 chr01 150 300 15 39 chr01 299 750 16...
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 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 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 ArticleHow Do You Get The Quality Score And Coverage For Every Single Position Of A...
Hi,I am trying to extract the coverage and the average quality score for each position of a reference assembly in bam/sam format. I have managed to get the coverage using BEDtools genomeCoverageBed...
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 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 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 ArticleExtract coverage per feature from a bam and bed to a file
Hi, a simple task.. or should be. I need to extract the average coverage per feature in a bam file. I have a genbank and bed file for the reference the bam was mapped to. if I map with e.g. Geneous...
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 ArticleGenbank to bed conversion for bedtools analysis
Hi, 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...
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