how to get -nms for bedtools
I'd like to merge bed files and preserve the names of the merged features using bedtools -nms option.However, this option (-nms) is deprecated in the newer bedtools.The documentation says I can use -o...
View ArticlePer Base Coverage
Is there a way to obtain per-base coverage for a define chromosome interval using a bam file generated from Illumina single-end reads? genomeCoverageBed in Bedtools does not seem to have an option for it.
View ArticleConverting Sam Files To Bam Files - Reproduce Results Nature Paper:...
I want to reproduce the results that people achieved in the following Nature paper: Transcriptome genetics using second generation sequencing in a Caucasian...
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.
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 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...
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Extract Only Paired-End Reads That Map A Specific Interval
Hi,Is it possible to extract paired-end reads that map to a specific interval ( from a bam file ). I tried with intersectBed :intersectBed -abam align.bam -b interval.gff3 -wa > result.bamhere's the...
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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 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 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...
View ArticleSamtools or Bedtools: How to filter a bam file with a bed file using strand...
HiI would like to filter a bam file, keeping only reads overlapping with genomic intervals from a bed file. I used samtools for this:samtools view -b -h -L bedfile.bed bamfile.bam However the -L option...
View ArticleVariant annotation using several .BED files
So, I have a data file containing several hundred variants in the following format: CHR # START POS END POS VARIANT ID 1 100 1000 rs1 1...
View ArticleHow To Count Genes In Genomic Regions Using A Gtf/Gff3 And A Bed File Of Regions
I'd like to count the number of unique genes in a gff file falling within a list of genomic regions. With bedtools I can count the number of regions within the gff which is almost what I want, but not...
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 ArticleHow To Combine Fpkm Values From Cufflinks With Contigs From De Novo Assembly...
Hi all,I am working on RNA-seq data analysis. I've finished running Tophat and Cufflinks to get FPKM values for each read from Illumina pair-end sequence. Also, parallely I've run Velvet to get contig...
View ArticleExtract coverage per feature from a bam and bed to a file
Hi, a simple task.. or should be. I need to extract the average coverage per feature in a bam file. I have a genbank and bed file for the reference the bam was mapped to. if I map with e.g. Geneous...
View ArticleTo Calculate The Exact Total Number Of Mapped Reads In Exome Regions
Dear All, I have some questions here. I want to do some quality control analysis on my exome data that are mapped on the reference genome. I am having the input bam file for a sample which contains...
View ArticleHow Do You Get The Quality Score And Coverage For Every Single Position Of A...
Hi,I am trying to extract the coverage and the average quality score for each position of a reference assembly in bam/sam format. I have managed to get the coverage using BEDtools genomeCoverageBed...
View ArticleRandom shuffling of features leaving gene models intact
I am looking for a tool that can randomly shuffle gff features into intergenic regions, but leaving the gene-models 'intact', so that at least all features of a gene are placed on the same contig and...
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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