Getting RNA sequences from gff and fa files
Hi. I have a folder full of .fa files, and a .gff. The gff file contains information about which loci look like they code for RNA sequences. The .fa contain the DNA sequences for a set of human...
View ArticleIntersect gene annotation with specific position or genomic interval
Hi,I've several genomic interval and I want to check if they are overlapping with known gene. I've a gtf file with the coordinates of gene exons. My idea was to use intersectBed from bedtools but I've...
View ArticleTool for binning windowBed output for K-means clustering
I have mapped high resolution ChIP-seq data to transcription start sites using windowBed. I now want to bin the data, in bin sizes of my choosing, relative to TSSs so that I can generate heat maps and...
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 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 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 each...
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 Articlehow to use bedtools windows to overlap upstream for positive strand strand
Hi,I am trying to use bedtools windows. It has been explained in the manual of the bedtools but I am still bit confused and thought a confirmation would be good. And I have no biological background.I...
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 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 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 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 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...
View ArticleGet the idea of splicing from reads mapped in RNA-seq
I've got a set of 100 bam files from a public experiment, I want to have an idea of splicing in each of them regarding three exons,without entering in some kind of depth-level procedure like Cufflinks...
View Articleusing GNU Parallel for bedtools
I am trying to run gnu:parallel on bedtools multicov function where the original command is bedtools multicov -bams bam1 bam2 bam3.. -bed anon.bed > Q1_Counst.bed I would like to implement the above...
View Articleidentify overlapping and non overlapping regions for paired-end data
gene1 gene2 chr1 25 30 chr1 34 37 chr1 15 20 chr1 25 28 chr1 80 90 chr1 10 13 gene1 gene2 chr1 25 30 chr1 36 39 chr1 15 20 chr1 18 20 chr1 80 90 chr1 19 22 common gene1 uniq gene2 (when we compare file...
View ArticleFinding overlapping variants (i.e. indels, snps) using annovar format.
Hello,I know that using bedtools functions (specifically intersect and windows), it is possible to find overlapping features in the two sets of data. The catch here is that bedtools only accept the...
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 ArticleExtracting genomic coverage information across different samples
Hello,I have 3 bam files that i wanted to compare against each other. For example i have reference file with 10,000 sequences. I have paired end reads sequenced for 3 different samples. 1) Sample 1 is...
View ArticleProblem with counting mapped reads
Hi, This is my very first experience analysing RNAseq data. My goal is to do differential analysis between two strains of a bacteria. So far, i managed to align and produce SAM and BAM files. I'm...
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