How to find the location of chromosome. Like Chr1, Chr2 etc
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FASTA file to Karyotype file
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.
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eennadi •
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The Last Word
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The Last Word
2 answers
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; }'
This tool looks cool for such https://github.com/galaxy-genome-annotation/galaxy-circos-tool
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