Hello,
I want to convert the VCF file with phase information into a phase block bed format.
So if this is the file:
#CHROM...
35 results in 0.0032 seconds.
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Convert vcf to bed based on PS field
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LiftOver h19 to canFam3
Hi all,
I am trying to convert hg19 coordinates to canFam3 coordinates ( in *.bed format obviously) but liftOver does not seem to work... -
Intersecting multiple bed files
Hello,
I have several RNA-Seq transcript data sets assembled and in BED format. I have masked out previously identified transcripts from... -
Count intervals of multiply mapped reads overlapping the genome
Hi everyone,
I have some SAM/BAM files containing the alignments of small RNA-seq reads to mm9 that are created by BWA. I'm interested... -
BEDOPS 2.4.3 released
BEDOPS 2.4.3 release (GitHub)
Compilation improvements
- Shane Neph put in a great deal of work to enable parallel builds (e.g.,
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how to feed de novo assembled transcripts to PhyloCSF
We have human de novo assembled transcripts. Those transcripts were assembled de novo without human genomic by using Trinity/Newbler. We want to use PhyloCSF...Last edited by emanlee; 05-24-2014, 07:50 PM. -
merge bed files
I have 2 bed files contain information about RNA-seq reads of two replicates for the same cell line, as follows:
http://www.ncbi.nlm.nih.gov/g... -
multiIntersectBed, or something like this
Hi,
I'm looking for overlapping regions from 3 (or more) bed files. multiIntersectBed from bedtools does that. However, I also want other... -
from gene symbols to a BED file with TSS positions
Hi all
I have a list of gene symbols (in excel or txt file) and I would like to get a BED file containing all the TSS positions of that... -
How to convert sam/bam or bed file into wig file
Hi,
How what tools can I use to convert sam/bam or bed file into a wig file? -
How does bedtools - bamToBed handle S operation in cigar string?
Hi,
I've been recently using bamToBed utility from the bedtools suite in order to transform the alignments in a BAM file into features... -
snpEff annotation
I am trying to understand genome trax download option bed and gff files.
What is the best tool for annotating vcf files with genome trax... -
BED to RefSeq gene format
Hello,
I would like to convert a BED interval file to RefSeq format. I need this to use it among with GATK DepthOfCoverage.
... -
Sort bed file by chr order and not lexicographically
I've been trying to sort a bed file with bedtools and bedops.
Both seem to sort the bed file lexicographically.
That means if... -
Convert pileup to bed
Hello,
I'm currently using samtools mpileup like this:
...Code:samtools mpileup -l target_regions.bed file1.bam file2.bam file3.bam
