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Bedtools 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...

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What 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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Counting 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...

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Filtering Bed Files By Using Bedops

hello every one,I have paired end illumina reads, R1.fastq and R2.fastq and I have mapped them as single-end reads by using bowtie2 default parameters, I performed further downstream analysis by using...

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Getting 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...

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Samtools or Bedtools: How to filter a bam file with a bed file using strand...

HiI would like to filter a bam file, keeping only reads overlapping with genomic intervals from a bed file. I used samtools for this:samtools view -b -h -L bedfile.bed bamfile.bam However the -L option...

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compute 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...

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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...

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Intersectbed: Return Reads In Fraction In Input Files

I have a question with respect to intersectBED and multiple input files:Is it possible to return reads which are present in, say 8/10 input files, without fractioning the reads in smaller...

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What 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...

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Extract 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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Multi Thread Bedtools

Hi,Is there a multi thread version of bedtools ? or is this feature in development ? Thanks,N.

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How To Combine Fpkm Values From Cufflinks With Contigs From De Novo Assembly...

Hi all,I am working on RNA-seq data analysis. I've finished running Tophat and Cufflinks to get FPKM values for each read from Illumina pair-end sequence. Also, parallely I've run Velvet to get contig...

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Heatmap Of Read Coverage Around Tsss

I am trying to plot a heatmap of read density around a feature of interest (TSSs) very common in genomics papers. something like this (B): However, I am struggling a bit in getting to look "right". A...

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Discrepancy 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...

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Bowtie2 Mapping Different Number Of Reads To Same Sequence When Ref-Seq Is...

I am using bowtie2 to map my PE reads. I have indexed multiple bacterial genomes by putting them together in a multi-fasta file fashion.bowtie2 -q -a -p 1 -x Multi -1 R100_1.fq -2 R100_2.fq -U...

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Bedtools: 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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Intersectbed/Coveragebed -Split Purify Exon?

all.reads.bam file records mapped RNA-seq reads data, including:exon:exon junctionexon bodyintron bodyexon:intron junctionQ1: When calculating RPKM for given RefSeq gene including all the position...

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Converting 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...

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Help With Exception When Using Bedtools Coveragebed With Paired Alignment....

I use bwa mem to align paired reads to few hundreds of microbial contigs; then I sort the alignment, and trying to get a coverage using bedtools genomecov -ibam alignments.paired.sorted.bam -bg...

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