How 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 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 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 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 ArticleGenomic Regions To Exclude Before Shuffling Intervals
I want to do permutation test: randomly reposit (shuffle) given genomic intervals and measure intersection between new coordinates and specific genomic element.Example: Different sets of genes: protein...
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 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 ArticleAnnotating Genomic Intervals
How can I annotate human genomic intervals (BED file) from a ChIP-seq experiment with information such as whether the interval overlaps with a gene(s)? Upstream of a gene? Overlaps with an exon?...
View ArticleConverting Gff To Bed With Bedtools?
I use bedtools's sortBed utility to sort BED files for various operations. It takes as input GFF files as well. However, when I feed it a GFF file as in:sortBed -i myfile.gffit outputs it as GFF, not...
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 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 ArticleDoes Bedtools Intersect -V Consider Unmapped Reads "As Not In B"
bedtools intersect -v -abam my.bam -b myregions.gff > notinmyregions.bamwould we see reads with 4 in the FLAG field - i.e. unmapped reads in notinmyregions.bam
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 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 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 ArticleGetting Number Of Reads In Intervals With Bedtools
What is the correct way to get the total number of reads strictly contained in each interval in a GFF from a BAM file while enforcing strandedness? What I am looking for is very close to this...
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 ArticleIntersectbed - Overlap Analysis Usign Vcf And Bed Files
I am trying to do an overlap analysis between 200 danish exomes (VCF courtsey: Zev) and 10 different gene regions. I would like to know what percentage overlaps between my region of interest (in...
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 ArticleIs It Possible To Filter Only Bookend Reads From A Bed File?
I have a bed file with many fragments, some overlapping, some on their own and some adjacent to each other (book-ended) features.I know can group overlapping and book-ended features using bedtools...
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