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...
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 ArticleUsing Gnu Parallel For Bedtools
I am trying to run gnu:parallel on bedtools multicov function where the original command is bedtools multicov -bams bam1 bam2 bam3.. -bed anon.bed > Q1_Counst.bedI would like to implement the above...
View ArticleBedtools Multicov Need A Bam Index File Specification Option
bedtools version 2.16.2 multicov used to compute the multiple sample coverage given a feature file(gtf bed).format: bedtools multicov -bams alin1.bam aln2.bam .. -bed capturRegion.bed...
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 ArticleFiltering Bed Files By Using Bedops
hello every one,I have paired end illumina reads, R1.fastq and R2.fastq and I have mapped them as single-end reads by using bowtie2 default parameters, I performed further downstream analysis by using...
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?...
View ArticleChanging Column Order In Bed File
Here is my data with A, B, C and D columns in my bed file. A. B. C. D. Chr 1. 1. 12. + Chr 2. 24. 56. +How can I move my D column to position 1 where the Column A right now?
View ArticleIntersect Gene Annotation With Specific Position Or Genomic Interval
Hi,I've several genomic interval and I want to check if they are overlapping with known gene. I've a gtf file with the coordinates of gene exons. My idea was to use intersectBed from bedtools but I've...
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 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...
View ArticleCounting 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...
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 ArticleBed 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 >...
View ArticleHow To Extract Scores From Bedgraph File Using Bed Tools
file1chr1 10 20 name 0 +file2chr1 12 14 2.5 chr1 14 15 0.5How could i extract average scores of file1 using file2, like below? I am trying to extract phastcons (file2) average scores of file1.chr1 10...
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 ArticleCreating Bed File For Lncrna Using Gencode Gtf File
Hi all,I want to get the bed file of lncRNA based on GENCODE GTF fileI download the file "gencode.v16.long_noncoding_RNAs.gtf.gz", and extract the chr, start, end info from the file, then I use...
View ArticleDetermining Each Samples Coverage Area
First time I am working with NGS data. I've got a BAM file with mapped reads for my samples and a BED file with the regions in HG19 that were targeted (used an Ion-torrent ampliseq panel). Are there...
View ArticleWhich Of The Genes Are Enriched With Repeat Elements
I would like to know which of my genes are enriched with repeats of LINE/SINE/ERV etc. elements. I have a bam file and the repeats in bed format. As far as I know BAM files contains aligned data for...
View ArticleTool For Binning Windowbed Output For K-Means Clustering
I have mapped high resolution ChIP-seq data to transcription start sites using windowBed. I now want to bin the data, in bin sizes of my choosing, relative to TSSs so that I can generate heat maps and...
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