assemble your own karyotype file

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9.7 years ago

cdwilliam524 ▴ 30

Hello,

Could anyone tell me how I could assemble my own karyotype file for circos plot? I am working on a bacteria project. The species is called Candidatus Kuenenia stuttgartiensis, which belongs to phylum/Clade Planctomycetes. I could not find the data from stuttgartiensis in UCSC table. I googled Ca. K stuttgartiensis's genome as well but found nothing. I combined all the contigs from this source and use it as the reference genome.

I have finished mapping through bwa, formatting through Samtools and merging overlapping sequences and generating coverage report through BEDTools.

Thanks in advance!

Will

circos karyotype file assemble karyotype • 2.5k views

ADD COMMENT • link updated 9.7 years ago by Biostar 20 • written 9.7 years ago by cdwilliam524 ▴ 30

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got anything? I am stuck on the same thing. Converting a FASTA to a karyotype file

ADD REPLY • link 7.7 years ago by The Last Word ▴ 230

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