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...
View ArticleIntersectbed Provides An Empty Output
Hi,I've downloaded the recent Cygwin version 1.7.24 and an trying to run bedTools but I get an empty file as my output. When I run the same commandline and files on a colleagues computer also through...
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 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 ArticleMulti Thread Bedtools
Hi,Is there a multi thread version of bedtools ? or is this feature in development ? Thanks,N.
View ArticleSplit A Bam File Into Several Files Containing All The Alignments For X...
Hi everyone! I am struggling with annotating a very big .bam file that was mapped using TopHat. The run was a large number of reads : ~200M. The problem is that when I now try to Annotate each read...
View ArticleTutorial: Piping With Samtools, Bwa And Bedtools
In this tutorial I will introduce some concepts related to unix piping. Piping is a very useful feature to avoid creation of intermediate use once files. It is assumed that bedtools, samtools, and bwa...
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 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 ArticleGetting Rna Sequences From Gff And Fa Files
Hi. I have a folder full of .fa files, and a .gff. The gff file contains information about which loci look like they code for RNA sequences. The .fa contain the DNA sequences for a set of human...
View ArticleHow To Create A Read Density Profile Within A Interval?
HI!I need some help: I have to create density profile with a window specific of 1kb (how many time a sequence is detected after NGS method). I have to use SAM and BEDtools, I think I can use genomeCov...
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 ArticleConvert Bamtobed Score
Hey,just a short question....is there a possibility to set the score in the bed file to "1" an not to the the alignment score?? arguments -tag and -ed only use BAM alignment tags... ?!? :/Cheers!
View ArticleExtracting Genomic Coverage Information Across Different Samples
Hello, I have 3 bam files that i wanted to compare against each other. For example i have reference file with 10,000 sequences. I have paired end reads sequenced for 3 different samples. 1) Sample 1 is...
View ArticleWhat Is The Fastest Method To Determine The Number Of Positions In A Bam File...
I have two very large BAM files (high depth, human, whole genome). I have a seemingly simple question. I want to know how many positions in each are covered by at least N reads (say 20). For now I am...
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 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 ArticleHow Can I Include One Bed File In Another Bed File ?
Hello, I have 2 bedfiles that share some common features let's call the first file A.bed (bigger file) and the second B.bed (smaller file). I would like to have a new bed file that includes everything...
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 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...
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