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Questions tagged [bed]

Browser Extensible Data, a collection of related plain text formats for describing genome features for visualization with genome browsers.

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How to convert bed to wig file!

I was wondering how can I convert bed file to wig file. I have several bed files which look like ...
Deb's user avatar
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2 votes
1 answer

CNVKit does not output all the accessible regions in the targets bed file

This question was also asked on Biostars I am using CNVkit on my data using hg38 as reference. The command that I am using is the following: ...
ashenflower's user avatar
1 vote
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tabix to subset each VCF by the coordinates given

I have a vcf file like below ...
Zizogolu's user avatar
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1 vote
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chip seq biological replicate merge after peak-calling

I have 3 biological replicates for KO condition. What I have done so far Peak calling The removed blacklisted region Now Im bit confused about the peak merging stage. Here Im trying to use the ...
kcm's user avatar
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How to get the splicing regions (BED) of all genes for Human GRCh38?

How can I obtain a BED file that describes the splicing sites of all genes for GRCh38 human genome ? Thank you
user324810's user avatar
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bedtools single-nucleotide coverage in BED-specified regions for multiple BAMs

I have a BED6 (BED + name, score, strand info) file that defines some regions of interest. I also have a set of BAMs corresponding to different samples. I would like to obtain output similar to <...
merv's user avatar
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