BEDTools "Segmentation fault" while working with genome.fa
I wanted to use BEDTools to extract genomic sequences (fastaFromBed).My BED file has all 24 chromosomes, hence I want to use whole genome (merged from chromosome.fa). Tried to: fastaFromBed -fi...
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...
View ArticleintersectBED: return reads in fraction in input files
I have a question with respect to intersectBED and multiple input files:Is it possible to return reads which are present in, say 8/10 input files, without fractioning the reads in smaller...
View ArticleAnnotating Genomic Intervals
How can I annotate human genomic intervals (BED file) from a ChIP-seq experiment with information such as whether the interval overlaps with a gene(s)? Upstream of a gene? Overlaps with an exon?...
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Reproduce ENCODE/CSHL Long RNA-seq data visualization viewed in UCSC, but...
MotivationThe 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 ArticleCounting 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...
View ArticleHow 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...
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 Articlecomparative SNP analysis
Hello, I am trying to compare the degree of A-to-G editing in a near-to-isogenic pair of cell lines. I have two biological replicates and have mapped with Bowtie and BWA, followed by a samtools mpileup...
View ArticleWhat is the best way to run bedtools in parallel with blocking
Say I am working on a server with a shared file system and 4 quad core nodes (I/O is not an issue, 16 cores total). I want to run coverageBed across 20 files. Currently I have a shell script that would...
View ArticleProblems extracting non-SNPs from a VCF file
Hello,In an SNP analysis, I am trying to extract those editing sites no found in the dbSNPs vcf file I have downloaded a couple of files (All SNPs and Common/Medical SNPs) from...
View Articlegetting all reads that align to a region in compact BED format using bedtools?
I'm trying to find all the reads (by name) from a BAM file that align to various regions in a bed file. Right now I can do this with bedtools using intersectBed:intersectBed -abam reads.bam -wo -f 1 -b...
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...
View Articleconverting GFF to BED with bedtools?
I use bedtools's sortBed utility to sort BED files for various operations. It takes as input GFF files as well. However, when I feed it a GFF file as in:sortBed -i myfile.gff it outputs it as GFF, not...
View ArticleHow to extract scores from BEDGraph file using BED tools
file1chr1 10 20 name 0 + file2chr1 12 14 2.5 chr1 14 15 0.5 How could i extract average scores of file1 using file2, like below? I am trying to extract phastcons (file2) average scores of file1.chr1 10...
View ArticleSimple redirection, I/O problem with bedtools
Hi Guys, Just a quick question. Its more of a Bash question rather than Bioinformatics, with Bedtools in question.I mostly pipe the bedtools I/O. Here's a general scenario :sed 1d fileA.bed |...
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 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 Articleraw counts from cufflinks output
Hi, I want to ask how to get the raw counts from the output of cufflinks. One way to do this is to use the fpkm.raw counts = FPKM * (length of that transcript/1000) * (# of mapped reads / 1e6)The FPKM...
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Profile Coverage of RNAseq samples?
Hi all,I have a quick question:How can I visualize aligned paired-end reads from RNAseq datasets in UCSC browser?I already mapped the reads and assembled the transcripts with Tophat/Cufflinks but I'm...
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