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Finding Overlapping Variants (I.E. Indels, Snps) Using Annovar Format.

Hello,I know that using bedtools functions (specifically intersect and windows), it is possible to find overlapping features in the two sets of data. The catch here is that bedtools only accept the...

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Different coverage from bedtools and in vcf file - HELP PLEASE

Dear all, I have trouble to understand how bedtools computing coverage. I have vcf file (generated from Illumina somatic caller) - I was created bed file from my vcf. Then I try to compute coverag with...

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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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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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How 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...

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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 >...

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N Closest Genes To A Given Location

Hi,This is basically an extension of the following question already asked in biostar (http://biostars.org/post/show/53561/python-finding-gene-closest-to-a-given-location/).Let us say I have a list of...

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Does 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

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Fastafrombed 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...

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Bedtools Compare Multiple Bed Files?

I've been dealing with comparison between two bed files using intersectBed -a -b command. I'm just wondering, is there any commands in Bedtools which can help us compare multiple bed files? Say, I have...

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GTF2/GFF3 "feature" types and expression analysis

Hi, I aligned a few samples using STAR to the genome provided in the Illumina iGenomes UCSC hg19 bundle (here) -- I used the provided gene feature (gtf2) file as is.  Now, my motive is to calculate the...

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Get The Idea Of Splicing From Reads Mapped In Rna-Seq

I've got a set of 100 bam files from a public experiment, I want to have an idea of splicing in each of them regarding three exons,without entering in some kind of depth-level procedure like Cufflinks...

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Per Base Coverage

Is there a way to obtain per-base coverage for a define chromosome interval using a bam file generated from Illumina single-end reads? genomeCoverageBed in Bedtools does not seem to have an option for it.

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How 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...

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How To Check Whole Genome With Bigwigsummary ?

Hi,I have question about bigwigsummary tools ,I have my start and end positions and my bigwig file but I want to check whole genome instead of chromosome by chromosome Is there any option to use this...

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macs and bedtools

HelloI have MACS2 output and now looking for peaks which are situated in introns. I have bed file with introns from USCS for my species. What file with peaks should I use for bedtools intersection?...

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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...

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How 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...

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Tutorial: Piping With Samtools, Bwa And Bedtools

In this tutorial I will introduce some concepts related to unix piping. Piping is a very useful feature to avoid creation of intermediate use once files. It is assumed that bedtools, samtools, and bwa...

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Reporting 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 |...

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