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Recent Replies
Answer: BED files
by
Alex Reynolds
35k
A simpler option is to use BEDOPS `bedmap`:
```
bedmap --echo --echo-map-id-uniq --delim '\t' <(cut -f1-3 enhancers.bed) ChIPseqs.bed > an…
Comment: BED files
by
Pierre Lindenbaum
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> but how can I be sure these are actually overlapping
uh ?
Answer: Why some insertions are symbolic in ALT column?
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LChart
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I don't know specifically about Sniffles2; but for other callers this typically means that the insert sequence itself couldn't be assembled…
Comment: The .vcf format: is there a file format better suited for the era of pangenomics
by
Vincent Laufer
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interesting answer, do you have any source that discusses this where i could read more?
Comment: The .vcf format: is there a file format better suited for the era of pangenomics
by
Vincent Laufer
★
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interesting answer and i like the reference to tile.DB.
with regard to 2. - this is the only place you and i might differ .. i think the p…
Answer: The .vcf format: is there a file format better suited for the era of pangenomics
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As a bit of a history: the VCF (and to an extent even the .bam format) came out of the research groups working on the 1000G project because…
Comment: BED files
by
lela2314
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I am trying this:
`bedtools intersect -a enhancer_liver2.bed -b chip_tfbs.bed -wb` because the transcription factor is in my second bed …
Comment: The .vcf format: is there a file format better suited for the era of pangenomics
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ChatGPT said
> VCF files can be extended to represent pangenome variant data by
> including information specific to each haplotype or gen…
Answer: The .vcf format: is there a file format better suited for the era of pangenomics
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[I can't help but be reminded of this XKCD strip][1].
1. Disagree. In my humble opinion, there is no such thing as an ideal data format,…
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@358a1a47
This is really timely work - two thoughts for consideration:
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Comment: BED files
by
lela2314
•
0
That is what I am doing but it does not seem to be working. I am doing:
bedtools intersect -a enhancer_muscle2.bed -b chip_tfbs.bed > …
Comment: The .vcf format: is there a file format better suited for the era of pangenomics
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Pierre Lindenbaum
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shameless LLM : https://ai.tinybio.cloud/chat
> The statement "VCF is the ideal file format for genomic information; no better file format…
Comment: BED files
by
Pierre Lindenbaum
155k
> I have been trying to solve
what did you try ? (... and your answer will contain `bedtools intersect`)
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