Question: FASTA file to Karyotype file
0
gravatar for The Last Word
2.7 years ago by
The Last Word170
India
The Last Word170 wrote:

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.

circos karyotype fasta • 1.7k views
ADD COMMENTlink modified 2.7 years ago • written 2.7 years ago by The Last Word170
5
gravatar for Sej Modha
2.7 years ago by
Sej Modha4.1k
Glasgow, UK
Sej Modha4.1k wrote:

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; }'

ADD COMMENTlink written 2.7 years ago by Sej Modha4.1k
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