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How 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...

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To 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...

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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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Bedtools To Compare A Vcf File From Samtools Mpileup With Dbsnp?

Hello,I have one big vcf file which is genereated by samtools mpileup by comparing 6 cell lines to see whether there are SNP differences between them.I would like to use bedtools for intersecting. How...

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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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Intersectbed Overlap

Hi,I've a question about intersectBed. Is it possible to extract only alignment like this :chromosome =============================================================== BED/BAM A ==============...

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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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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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Counting Number Of Bam Reads Directly Within Set Of Intervals With Bedtools

how can I count the number of BAM reads falling directly within a set of intervals, given in a GFF format? Note that I do not want reads overlapping the intervals, but ones that fall directly within...

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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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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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Convert .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...

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Coveragebed, Depth/Breadth Of Coverage

I'm using coverageBed to calculate the depth and breadth of coverage, but I'm not sure I'm doing this right. I want to calculate the two values for each human chromosome. For example, I've created a...

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Reproduce Encode/Cshl Long Rna-Seq Data Visualization Viewed In Ucsc, But...

Motivation The ENCODE data comes out, and luckily they provide both .bam file and .bigwig file. Thus, it occurs to me that I want to give a try to reproduce the data visualization with tool: BEDtools...

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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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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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Running BedTools on Linux Cluster: Permission Denied

I been having some problems with running BedTools binaries in a linux cluster. I have the binaries in my own $HOME/bin file and when I try to run bedtools I get this error messageĀ  -bash: bedtools:...

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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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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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Bedgraph Not Displayed In Igv

Hi, I am new and so facing problem. I was trying to make a bed graph file using bed tools genomecov command. The command was: bedtools genomecov -ibam filename.sorted.bam -g chromosome sizes.txt >...

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