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6.5 years ago
maxwells_daemon
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10
I need help understanding how to convert these file types to the template that Circos accepts. Please comment and I will provide more detail. Thank you.
The types of files Circos accepts are of the following notation:
chr - hs1 1 0 247249719 green
chr - hs2 2 0 242951149 green
chr - hs3 3 0 199501827 green
chr - hs4 4 0 191273063 green
chr - hs5 5 0 180857866 green
chr - hs6 6 0 170899992 green
chr - hs7 7 0 158821424 green
chr - hs8 8 0 146274826 green
This is the data types I have:
FAA file:
>ORF1_1 seq1 2300..2602 DNA binding protein
MSNKYPVAYAVGQKIKSLRKSQGYTVFQLAKEIDISEQQLFRYERGVNRIDIDCLVKVLDVLGINIGNFF
EDVMGGMVDVPENNEQHIPAHFDNKALSIF
PTT file:
Location Strand Length PID Gene Synonym Code COG Product
2300..2602 + 100 1834182688 - ORF1_1 - - DNA binding protein
3171..3938 - 255 1834182689 - ORF1_2 - - Hydrogen sulfide production: membrane anchoring protein
3935..4513 - 192 1834182690 - ORF1_3 - - Molybdopterin oxidoreductase, Psr/Psh family, PsrB-like Fe-S subunit
4528..6807 - 759 1834182691 - ORF1_4 - - Thiosulfate reductase
7589..8392 - 267 1834182692 - ORF1_5 - - Conserved protein YunE
.txt file for antitoxins and toxins:
Location Strand ID Gene Locus_tag Length(aa) Type blastp_subject subject_domain subject_family blastp_identity blastp_evalue h_value query_annotation subject_annotation
637603..637929 - ORF13_1 - ORF13_1 108 toxin 197287170 RelE relE-like_domain 97.22 2e-74 97.22 Plasmid stabilization system protein plasmid stabilization protein [Proteus mirabilis HI4320]
637935..638204 - ORF13_2 - ORF13_2 89 antitoxin 197287171 PHD PHD-like_domain 97.75 9e-58 97.75 Antitoxin antitoxin [Proteus mirabilis HI4320]
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How do I convert the files of these types to the other in a way that Circos accepts and makes sense?
Comment to provide more detail. Please elaborate on the format you need.
Well, what do you want to show?
I want to show an outer ring with the genome, inner ring with aligned toxin-antitoxin pairs, and prophage regions. I used CGView before, but I need to use Circos.