Coveragebed, 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 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 ArticleRaw Counts From Cufflinks Output
Hi, I want to ask how to get the raw counts from the output of cufflinks. One way to do this is to use the fpkm.raw counts = FPKM * (length of that transcript/1000) * (# of mapped reads / 1e6)The FPKM...
View ArticleBedtools intersect tab and bed files
How can you call Bedtools intersect on a tab and bed file? without getting the typical:"Differing number of BED fields encountered at line: #. Exiting..."Error.My bed file has 15 columns and my tab...
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 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 ArticleReproduce Encode/Cshl Long Rna-Seq Data Visualization Viewed In Ucsc, But...
Motivation The ENCODE data comes out, and luckily they provide both .bam file and .bigwig file. Thus, it occurs to me that I want to give a try to reproduce the data visualization with tool: BEDtools...
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 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 ArticleHow To Find The Closest Distance From Bed Files Between Genes And Repeats...
How can I use the closestBed from bedtools to find the closest locations between two bed files. The important bit here is that i want them to be upstream and in correct oriantation.When I use the -s...
View ArticleIntersectbed/Coveragebed -Split Purify Exon?
all.reads.bam file records mapped RNA-seq reads data, including:exon:exon junctionexon bodyintron bodyexon:intron junctionQ1: When calculating RPKM for given RefSeq gene including all the position...
View ArticleConvert .Txt Into Bed Files
I used paired-end sequence data for copy number variation study; and eventually get .txt files as output. I'm hoping to use Bedtools to compare my results with others. Can I convert .txt files into...
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 ArticleReporting The Bam Reads Overlapping A Set Of Intervals With Bedtools
I am trying to use bedtools to pull out the reads falling directly within a set of BED coordinates. While this command does it successfully:intersectBed -abam mybam.bam -b intervals.gff -wa -wb -f 1 |...
View ArticleGenbank to bed conversion for bedtools analysis
Hi, I need to use bedtools to obtain the coverage across two bam files for comparison. However, to do this, I need a .bed file of the genome features (of the reference genome used to generate the...
View ArticleCalculating Exome Coverage
*// Edit to make the post more clear (Mapping done via Bowtie2). My problem is that when counting Exome Coverage via coverageBed gives different results than via genomeCoverageBed. So I'm not sure if...
View ArticleHow To Get Annotation For Bed File From Another Bed File
Hello All,I have a bed file (with Chr, Start, End, Name, Score and Strand) Chr1 5678 5680 NA 7 + Chr1 700 800 NA 8 - Chr1 900 1200 NA 10 -and would like to know, how can I get the annotation for the...
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 ArticleHelp With Exception When Using Bedtools Coveragebed With Paired Alignment....
I use bwa mem to align paired reads to few hundreds of microbial contigs; then I sort the alignment, and trying to get a coverage using bedtools genomecov -ibam alignments.paired.sorted.bam -bg...
View ArticleIntersectbed Overlap
Hi,I've a question about intersectBed. Is it possible to extract only alignment like this :chromosome =============================================================== BED/BAM A ==============...
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