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bioinfo-chru-strasbourg / vcf2circos

python plotly Circos from VCF
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Support for human T2T assembly #39

Open bwlang opened 7 months ago

bwlang commented 7 months ago

I was not able to find the expected input files for construction of the assembly.

(https://hgdownload.soe.ucsc.edu/gbdb/hs1/ does not seem to have ncbiRefSeqCurated.txt.gz, chromInfo.txt.gz, cytoBand.txt.gz).

is there an alternative using the bigbed files that they do have? e.g. https://hgdownload.soe.ucsc.edu/gbdb/hs1/bbi/ncbiRefSeqCurated.bb https://hgdownload.soe.ucsc.edu/gbdb/hs1/hubs/chromAlias.txt https://hgdownload.soe.ucsc.edu/gbdb/hs1/cytoBandMapped/cytoBandMapped.bb

Thanks for any advice...

thomasguignard commented 4 months ago

Hello, You can first transform bigbed files to bed with this ucsc application: https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/bigBedToBed e.g. bigBedToBed ncbiRefSeqCurated.bb ncbiRefSeqCurated.bed

Then sort as recommended: sort -k1,1V -k2,2n ncbiRefSeqCurated.bed > ncbiRefSeqCurated_sort.bed