Hi all
Actually, I need chromosome start and end positions (10 chromosomes/Brassica rapa) and I have genome sequences in fasta file format. In the file, for each chromosome, it is mentioned like this...chr1=1:XXXXX; chr2=1:XXXXX and goes on. I have searched for BED file format and I also tried some format conversion (to BED file), but no success. Can anyone help me in this regards? Should I consider the end position of Chr1 as the start position of Chr2? Your recommendations and suggestions will be highly appreciated.
Thanks
In my personal experience, I found chr2 start from ch2 = 1:XXXX also similarly chr3 and so on. I find this fine. Only problem I faced was during indexing so I just split my data by chromosome and it worked for me.
Article Comparative genomic analysis of the compound Brassica napus Rf locus
Dear Muthusamy Muthusamy ,
I found one way to get coordinates from fasta file. Just change file.fa with your fasta file and you will have coordinates for your genome.
Good luck..!!
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