FASTA file to Karyotype file

Question

[The Last Word]

I am trying to use Circos and in order to do so, I have to convert my FASTA file into a Karyotype input file. Is there any way to do so? I know that there is another similar question which was asked two years ago but I am looking for any update that might have come in the past two years to make this easier. Also, is there a methodology to compare two transcriptomes in Circos. I have noticed papers with comparisons shown in the form of circos images. If Circos only accepts a karyotype file at a time, how is that done? I am relatively new to Circos and hence all the questions. Please help.

Answer 1

[Sej Modha]

You could use simple bash solution to convert a fasta file to a karyotype file by parsing the header and the size of the fasta sequences. Following awk command would do the job and would print fastsa headers as column 3 and 4 for label and identifier for each sequence. cat file.fa | awk '$0 ~ ">" {print c; c=0;printf "chr - " substr($0,2,100) " " substr($0,2,100) " " "0" " "; } $0 !~ ">" {c+=length($0);} END { print c; }'

[tothepoint]

How to find the location of chromosome. Like Chr1, Chr2 etc

Answer 2

[eennadi]

This tool looks cool for such https://github.com/galaxy-genome-annotation/galaxy-circos-tool