I was assuming that paired information was deduced and included in the amos .afg file during its generation, but actually the paired information must be explicitly provided in a separate .mates file. Once this was included in the .afg file generation, I could run minimus -> bambus -> hawkeye to view any scaffolds.
I found a really helpful site which provided a script to parse out the mate pair information from your input .fasta file here http://compbio.korea.ac.kr/wiki/inde...ina_for_bambus which is this:
Code:
cat my.fasta |grep ">" |sed s/\>//g |sed 's/\/1*$/./g;s/\/2*$/./g'|awk -F "." '{print $1}' |sort |uniq -c |awk '{if ($1 == 2) print $2"/1\t"$2"/2\tsmall"}' > mates.txt
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