unmapped reads

[asylvz]

Hello,

I'm wondering if there is an option to output unmapped reads?

Thank you, Arda

[maickrau]

There is no option but if you have alns.gaf and reads.fa then you can find the unmapped reads with:

cut -f 1 < alns.gaf | uniq | cat - <(grep '>' < reads.fa | tr -d '>') | sort | uniq -c | grep -P '^\s+1' | sed 's/^\s\+1\s//g'