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Building variant from bed file #200

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jawad9-11 opened this issue Nov 21, 2024 · 3 comments
Open

Building variant from bed file #200

jawad9-11 opened this issue Nov 21, 2024 · 3 comments

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@jawad9-11
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i have a catalogue in the form of bed file look like this:
chr1 12061 12071 5 GGAGT
chr1 14661 14673 6 GTCTGG
chr1 14709 14722 6 GTCCTC
chr1 14734 14741 3 GCT
chr1 15241 15255 6 GGGCCA
chr1 15384 15395 6 GCAGGC
chr1 15614 15624 4 CAGG
now i want to create a cataloge in json format. can you explain to me like LocusId: "is it gene name" so first i have to annotate the file or what?
can you explain the work path to me? Thank You

@andreasssh
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You can easily convert BED file to JSON via this webpage or use bed_to_catalog.py from this repository

@jawad9-11
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You can easily convert BED file to JSON via this webpage or use bed_to_catalog.py from this repository

Thank you for your answer but I want to ask as you have named the locus id as a gene name. but there are also intergenic regions can you tell me what should to do with them or just name them like this :
LocusId": "chr10-100000049-100000054

@andreasssh
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You can use any name for LocusId. The BED -> JSON conversion scripts are using coordinates as the locus id so it would be easy to understand later what region it is, and if you wish, annotate them with gene names, etc. as you have the coordinates.

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