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...
View ArticleHow To Get All Entries Of B With Bedtools
Hi All, Is there any way to get all the original B entry(even the ones for which there is no overlap with A as well) in intersectBed utility? I am trying to overlap two bed files. I need all the entry...
View ArticleHelp 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...
View ArticleCoveragebed, 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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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...
View ArticleDoes 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 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 ArticleMulti Thread Bedtools
Hi,Is there a multi thread version of bedtools ? or is this feature in development ? Thanks,N.
View Articlebedtools: extracting no coverage regions
Hello,I am not sure if this has been answered before as I looked and couldn't find a simple answer.I have a bam file, and all I want is to annotated all regions with 0 coverage in bed format. Is that...
View ArticleHow To Get Fasta Format Using Fastafrombed Or How To Turn Linearized Fasta To...
I extracted sequences with fastaFromBed and have no complains about the BEDTools which is really awesome thing.Otherwise extracted sequences look like this:>chr19:13985513-13985622...
View ArticleHeatmap 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...
View ArticlePicking Random Genomic Positions
I do have a set of TF binding coordinates and want to see if there is any significant overlap with an open chromatin annotation.Example of TF coord: chr1 19280 19298 chr1 245920 245938 chr2 97290 97308...
View ArticleGetting 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...
View ArticleBedtools 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...
View ArticleBowtie2 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...
View ArticleTool: 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...
View ArticleIs It Possible To Filter Only Bookend Reads From A Bed File?
I have a bed file with many fragments, some overlapping, some on their own and some adjacent to each other (book-ended) features.I know can group overlapping and book-ended features using bedtools...
View ArticleGet 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...
View ArticleBed 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...
View ArticleN 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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