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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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Question about number of reads within intervals

Hi there, This question is very basic but I need to ensure that I'm going on the right way. I need to calculate the number of reads falling inside my bed intervals and the number of reads falling...

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General Considerations For Genomic Overlaps?

Hello I was wondering about general considerations for performing overlap of genomic regions and doing Monte Carlo-type statistics. Below I have made a description of how I do it, unfortunately Im not...

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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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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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Bed 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...

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How To Get Annotation For Bed File From Another Bed File

Hello All,I have a bed file (with Chr, Start, End, Name, Score and Strand) Chr1 5678 5680 NA 7 + Chr1 700 800 NA 8 - Chr1 900 1200 NA 10 -and would like to know, how can I get the annotation for the...

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Tool: Bedtools: Analyzing Genomic Features

All practicing bioinformaticians will face problems that require them to compare, query and select genomic features across an entire genome. As it happens efficient interval representation and query is...

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Intersectbed Tool Generating Empty File

I have used the Bedtools command intersectBed to check the overlap between two bed files. A is my INDEL file and B is my Reference file. But it is producing an empty output file. I thought the problem...

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Intersectbed - 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...

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Extract Only Paired-End Reads That Map A Specific Interval

Hi,Is it possible to extract paired-end reads that map to a specific interval ( from a bam file ). I tried with intersectBed :intersectBed -abam align.bam -b interval.gff3 -wa > result.bamhere's the...

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Convert 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!

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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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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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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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Getting 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...

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How To Extract Scores From Bedgraph File Using Bed Tools

file1chr1 10 20 name 0 +file2chr1 12 14 2.5 chr1 14 15 0.5How could i extract average scores of file1 using file2, like below? I am trying to extract phastcons (file2) average scores of file1.chr1 10...

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Merging/Intersecting Different Gene Annotations - Should I Extend Coordinates?

I want to create gene data-set (as big as possible), hence I am using several gene annotations. However, genes in different annotations overlap (it's the same gene). For reducing biases I overlap...

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Getting Number Of Reads In Intervals With Bedtools

What is the correct way to get the total number of reads strictly contained in each interval in a GFF from a BAM file while enforcing strandedness? What I am looking for is very close to this...

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