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Creating Bed File For Lncrna Using Gencode Gtf File

Hi all,I want to get the bed file of lncRNA based on GENCODE GTF fileI download the file "gencode.v16.long_noncoding_RNAs.gtf.gz", and extract the chr, start, end info from the file, then I use...

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Comparative Snp Analysis

Hello, I am trying to compare the degree of A-to-G editing in a near-to-isogenic pair of cell lines. I have two biological replicates and have mapped with Bowtie and BWA, followed by a samtools mpileup...

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Bedtools 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...

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Convert Bamtobed Score

Hey,just a short question....is there a possibility to set the score in the bed file to "1" an not to the the alignment score?? arguments -tag and -ed only use BAM alignment tags... ?!? :/Cheers!

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how to get -nms for bedtools

I'd like to merge bed files and preserve the names of the merged features using bedtools -nms option.However, this option (-nms) is deprecated in the newer bedtools.The documentation says I can use -o...

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How Can I Merge Intervals ?

Hello everybody, I should be grateful if you would kindly help me de fix my problem. I have a table like that :Chromosome start end info1 info2 chr01 1 100 15 35 chr01 150 300 15 39 chr01 299 750 16...

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How 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...

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Bed File Bedpe Format

Hi,I'm having trouble with converting the bam file into bed -bedpe using the bedtools.workflow: samtools sort -n mut.bam mut.Namesorted bamTobed -i mut.Namesorted.bam -bedpe >...

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Different coverage from bedtools and in vcf file - HELP PLEASE

Dear all, I have trouble to understand how bedtools computing coverage. I have vcf file (generated from Illumina somatic caller) - I was created bed file from my vcf. Then I try to compute coverag with...

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How Can I Include One Bed File In Another Bed File ?

Hello, I have 2 bedfiles that share some common features let's call the first file A.bed (bigger file) and the second B.bed (smaller file). I would like to have a new bed file that includes everything...

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how to run subtract command in java

I want to run subtract command in java, could somebody tell me how to use.Thank you very much.

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Given gene ID and genomic coordinates, how can I create a GFF formatted file?

  I have downloaded a list of coordinates of yeast genes from Xu et al., 2009 (see table S3). Unfortunately its current format is not a standard format so it does not appear to be compatible with the...

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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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How 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...

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Intersectbed 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...

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Bedtools Compare Multiple Bed Files?

I've been dealing with comparison between two bed files using intersectBed -a -b command. I'm just wondering, is there any commands in Bedtools which can help us compare multiple bed files? Say, I have...

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How 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...

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Genbank 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...

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Simple Redirection, I/O Problem With Bedtools

Hi Guys, Just a quick question. Its more of a Bash question rather than Bioinformatics, with Bedtools in question.I mostly pipe the bedtools I/O. Here's a general scenario :sed 1d fileA.bed |...

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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...

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