Discrepancy 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 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 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 ArticleClik here to view.
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 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 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 ArticleBedtools on Cygwin problem.
Hi I'm trying to install the latest release of Bedtools via Cygwin but there's a weird error during process. I know this isn't the best solution, but I do not have an other choice. Perhaps anyone...
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...
View ArticleGTF2/GFF3 "feature" types and expression analysis
Hi, I aligned a few samples using STAR to the genome provided in the Illumina iGenomes UCSC hg19 bundle (here) -- I used the provided gene feature (gtf2) file as is. Now, my motive is to calculate the...
View ArticleBedtools: Top N Most Similar Regions When Comparing Two Bed/Wig/Bam Files?
Is there an easy way of finding, probably with bedtools, given a window size, the top N most correlated regions when comparing two bed/wig files? For example, in comparing two bed/wig/bam files that...
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 ArticleMulti Thread Bedtools
Hi,Is there a multi thread version of bedtools ? or is this feature in development ? Thanks,N.
View ArticleSplice Junction file intersection with genome annotation
Hello, I have a tab delimited format Splice Junction file and the file looks something like this: chr1 11212 12009 1 1 0 0 2 48 chr1 11672 12009 1 1 0 0 1...
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...
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 ArticleDoes Windowbed Extend Reads?
I am using WindowBed, part of the BedTools suite, to align reads to a reference file and I obtained a very interesting result. I am trying to rule out an analysis artifact that could be caused by...
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 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 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 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 Article