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Get 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...

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Split A Bam File Into Several Files Containing All The Alignments For X...

Hi everyone! I am struggling with annotating a very big .bam file that was mapped using TopHat. The run was a large number of reads : ~200M. The problem is that when I now try to Annotate each read...

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Identify 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...

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Problem 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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bedtools: extracting no coverage regions

Hello,I am not sure if this has been answered before as I looked and couldn't find a simple answer.I have a bam file, and all I want is to annotated all regions with 0 coverage in bed format. Is that...

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Raw 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...

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Converting Sam Files To Bam Files - Reproduce Results Nature Paper:...

I want to reproduce the results that people achieved in the following Nature paper: Transcriptome genetics using second generation sequencing in a Caucasian...

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Getting Unmapped Reads: Comparing Fastq To Bam

given a FASTQ file and a BAM file of aligned reads, is there an efficient way to get all FASTQ reads that are in the original FASTQ but not in the BAM? Perhaps using bedtools. i.e.:unmapped_script...

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Correlation Of Fpkm And Length Normalized Transcript Mapped Read Count

Hello, in the process of estimating expression for a 16 human tissue dataset ("Human Body Map 2.0 GSE30611") I used different methods to estimate the expression of the genes. After mapping against hg19...

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Does 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...

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Intersect 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...

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How To Rearrange Paired End Bam File?

Hello all,I have a paired end bam file and I want to use bedtools for them. After merging, the paired end read alignments are not lying next to each other. It is making problems in the bedtools...

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Intersectbed 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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Bedtools subtract not dealing well with large datasets

I am using bedtools subtract with large datasets and it keeps crashing, giving the following error    terminate called after throwing an instance of 'std::bad_alloc'Is there a way to get over this...

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Heatmap 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...

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Bedtools To Compare A Vcf File From Samtools Mpileup With Dbsnp?

Hello,I have one big vcf file which is genereated by samtools mpileup by comparing 6 cell lines to see whether there are SNP differences between them.I would like to use bedtools for intersecting. How...

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To 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...

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Intersectbed - 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...

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How 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...

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Reproduce 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...

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