How 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 ArticleHow To Get All Entries Of B With Bedtools
Hi All, Is there any way to get all the original B entry(even the ones for which there is no overlap with A as well) in intersectBed utility? I am trying to overlap two bed files. I need all the entry...
View ArticleHeatmap 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...
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 ArticleFastafrombed 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 ArticleCoveragebed, Depth/Breadth Of Coverage
I'm using coverageBed to calculate the depth and breadth of coverage, but I'm not sure I'm doing this right. I want to calculate the two values for each human chromosome. For example, I've created a...
View ArticleHow Can I Compare And Merge Bed Files
I have three bed files with chrNo, start, end position and type. I need to compare each chrNo, start and end position of one file with 2 other files and write the common one in a new file. Can any one...
View Articlecompute normal-tumor coverage ratio from exome BAMs
Could someone please suggest a quick way to compute the data ratio of uniquely mapped reads in the normal to uniquely mapped reads in the tumor, as required by Varscan in the command below? I have over...
View ArticleMerging/Intersecting Different Gene Annotations - Should I Extend Coordinates?
I want to create gene data-set (as big as possible), hence I am using several gene annotations. However, genes in different annotations overlap (it's the same gene). For reducing biases I overlap...
View ArticleBed File Of Mapq Sliding Window On A Bam File?
There may already be a recipe for this, so asking first before reinventing the wheel: I would like to create a bed file where the score is the average mapQ from the reads of the input.bam file. I think...
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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...
View ArticleBedtools "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 ArticleBedgraph Not Displayed In Igv
Hi, I am new and so facing problem. I was trying to make a bed graph file using bed tools genomecov command. The command was: bedtools genomecov -ibam filename.sorted.bam -g chromosome sizes.txt >...
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 ArticlePicking Random Genomic Positions
I do have a set of TF binding coordinates and want to see if there is any significant overlap with an open chromatin annotation.Example of TF coord: chr1 19280 19298 chr1 245920 245938 chr2 97290 97308...
View ArticleHow To Find The Nearest Gene To A Retrotransposon Insert?
Hi,I have a BED file with the position of retrotransposons in the mouse genome and I would like to find the nearest gene, the distance to that gene and whether it is on the + or - strand. There are so...
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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 ArticleMulti Thread Bedtools
Hi,Is there a multi thread version of bedtools ? or is this feature in development ? Thanks,N.
View Articlemacs and bedtools
HelloI have MACS2 output and now looking for peaks which are situated in introns. I have bed file with introns from USCS for my species. What file with peaks should I use for bedtools intersection?...
View Articlebedtools intersect - something wrong with chromosome numbers >= 10?
Hi!I have an alignment (.bam) of reads to mm9 genome. I sorted it with samtools sort, so that later I can use -sorted key with bedtools. I also created a .bed-file with regions of interest, in which I...
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