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Converting BAM to bedGraph for viewing on UCSC?
I'm trying to go from a BAM file to a representation viewable in UCSC, ideally bedGraph. I am trying to use Bedtools's genomeCoverage like this: genomeCoverageBed -ibam accepted_hits.sorted.bam -bg...
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 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 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 ArticleDiscrepancy in samtools mpileup/depth and BEDTools genomeCoverageBed counts
I am getting different counts for the number of bases on reference covered by aligned reads using samtools depth/mpileup and BEDTools genomeCoverageBed commands. I am using samtools-0.1.19 and...
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 ArticleBedtools genomeCoverageBed usage : How to create a genome file?
I am using BEDTOOLS and the following command to get the coverage file:$ ./genomeCoverageBed -ibam ~/GG_project/trim/ecoli.bam -g > ~/GG_project/trim/coveragewhere ecoli.bam is my sorted bam file,...
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 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 ArticleHow to rearrange paired end bam file?
Hello all,I have a paired end bam file and I want to use bedtools for them. After merging, the paired end read alignments are not lying next to each other. It is making problems in the bedtools...
View ArticleGetting the average coverage from the coverage counts at each depth.
Hi,I have read quite a few posts here about coverage already. But I still had a few questions. I have a BAM file I'm trying to find the coverage of it (typically like say 30X).So, I decided to use...
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 Articlebedtools multicov need a index 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 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 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...
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 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 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...
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Heatmap of read coverage around TSSs
I am trying to plot a heatmap of read density around a feature of interest (TSSs) very common in genomics papers. something like this (B):However, I am struggling a bit in getting to look "right". A...
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