Does 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 Article"mask" values in a bedgraph
I am trying to plot average conservation in a list of genomic features, and so far managed to do it successfully using a combination of the phastCons bigwig files (hg19.100way.phastCons.bw) and...
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 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 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 ArticleUsing Gnu Parallel For Bedtools
I am trying to run gnu:parallel on bedtools multicov function where the original command is bedtools multicov -bams bam1 bam2 bam3.. -bed anon.bed > Q1_Counst.bedI would like to implement the above...
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 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 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 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 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 ArticleConverting Sam Files To Bam Files - Reproduce Results Nature Paper:...
I want to reproduce the results that people achieved in the following Nature paper: Transcriptome genetics using second generation sequencing in a Caucasian...
View Articleerror 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 ArticleBedtools: Top N Most Similar Regions When Comparing Two Bed/Wig/Bam Files?
Is there an easy way of finding, probably with bedtools, given a window size, the top N most correlated regions when comparing two bed/wig files? For example, in comparing two bed/wig/bam files that...
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Converting Bam To Bedgraph For Viewing On Ucsc?
I'm trying to go from a BAM file to a representation viewable in UCSC, ideally bedGraph. I am trying to use Bedtools's genomeCoverage like this: genomeCoverageBed -ibam accepted_hits.sorted.bam -bg...
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 ArticleGetting All Reads That Align To A Region In Compact Bed Format Using Bedtools?
I'm trying to find all the reads (by name) from a BAM file that align to various regions in a bed file. Right now I can do this with bedtools using intersectBed:intersectBed -abam reads.bam -wo -f 1 -b...
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 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 ArticleHow To Rearrange Paired End Bam File?
Hello all,I have a paired end bam file and I want to use bedtools for them. After merging, the paired end read alignments are not lying next to each other. It is making problems in the bedtools...
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