error with bedtools slop
Hi, I am trying to run a bedtools slop on my.bed file and hg19.genomebedtools slop -i H3K27me3.bed -g hg19.genome -b 30I get the following error:Less than the req'd two fields were encountered in the...
View ArticleBedtools intersect tab and bed files
How can you call Bedtools intersect on a tab and bed file? without getting the typical:"Differing number of BED fields encountered at line: #. Exiting..."Error.My bed file has 15 columns and my tab...
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 ArticleGTF2/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...
View ArticleCalculate reciprocal overlap for thousands of samples
I have around 20k samples with BED files. How can I calculate reciprocal overlap for each segment? I want to find all segments with 50% reciprocal overlap or better.Â
View ArticleHow 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...
View ArticleBedtools: 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...
View ArticleIntersectbed - 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...
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 ArticleReporting 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 |...
View ArticleReproduce 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...
View ArticleHow 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...
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 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 ArticleBedtools 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...
View ArticleCorrelation Of Fpkm And Length Normalized Transcript Mapped Read Count
Hello, in the process of estimating expression for a 16 human tissue dataset ("Human Body Map 2.0 GSE30611") I used different methods to estimate the expression of the genes. After mapping against hg19...
View ArticleGetting 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 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 ArticleMemory Efficient Bedtools Sort And Merge With Millions Of Entries?
I would like to know if there is a memory-efficent way of sorting and merging a large amount of bed files, each of them containing millions of entries, into a single bed file that merges the entries,...
View ArticleCan Bedtools/Bedops Used To Extract Regions Where Scores Are Higher Than A...
I have a very basic question about bedtools and bedops. Can I use these tools to filter all the regions where the score is higher (or lower) than a given value? For example, let's say that I have a BED...
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