Annotating Genomic Intervals
How can I annotate human genomic intervals (BED file) from a ChIP-seq experiment with information such as whether the interval overlaps with a gene(s)? Upstream of a gene? Overlaps with an exon?...
View ArticleTo Group Items In Bed Files
For example, we now have a bed file:chr1 23455 45678 chr1 23446 45663 chr1 23449 45669 chr1 30000 31000Is there anyway to group the first three lines, while leaving the last line alone? I know Bedtools...
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 ArticleWhat Is The Best Way To Run Bedtools In Parallel With Blocking
Say I am working on a server with a shared file system and 4 quad core nodes (I/O is not an issue, 16 cores total). I want to run coverageBed across 20 files. Currently I have a shell script that would...
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 ArticleDoes Bedtools Intersect -V Consider Unmapped Reads "As Not In B"
bedtools intersect -v -abam my.bam -b myregions.gff > notinmyregions.bamwould we see reads with 4 in the FLAG field - i.e. unmapped reads in notinmyregions.bam
View ArticleReporting The Bam Reads Overlapping A Set Of Intervals With Bedtools
I am trying to use bedtools to pull out the reads falling directly within a set of BED coordinates. While this command does it successfully:intersectBed -abam mybam.bam -b intervals.gff -wa -wb -f 1 |...
View ArticleBed File Of Mapq Sliding Window On A Bam File?
There may already be a recipe for this, so asking first before reinventing the wheel: I would like to create a bed file where the score is the average mapQ from the reads of the input.bam file. I think...
View ArticleSnps Comparison
Hello,I would like to compare SNPs from different methods:number of SNPsSNPs postion (position where method A has SNPs but not B and vice versa. Where both have SNPs)I would be interested to get a...
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How To Explain Uneven Coverage Of A Dna Seqment Obtained Via Pcr Amplification.
Experiment: deep sequencing for mutants in 700nt fragment.the fragment of dna was preamplified by primers flanking the fragment followed by hiseq.per base coverage was calculated by coverageBed -d...
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 Articlebedtools: extracting no coverage regions
Hello,I am not sure if this has been answered before as I looked and couldn't find a simple answer.I have a bam file, and all I want is to annotated all regions with 0 coverage in bed format. Is that...
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 ArticleFastafrombed 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 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 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 ArticleIntersectbed Provides An Empty Output
Hi,I've downloaded the recent Cygwin version 1.7.24 and an trying to run bedTools but I get an empty file as my output. When I run the same commandline and files on a colleagues computer also through...
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...
View ArticleBedtools 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 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...
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