Create mate file from illumina for bambus

From CSBLwiki

This script i got from Sergey Koren from AMOS, (which i adapted a bit):

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

You need to put in the fasta file with the read names as 'my.fasta'.

The file 'my.fasta' requires filenames to end with /1 and /2. If you have other file names, like .x and .y. You should replace;

sed 's/\/1*$/./g;s/\/2*$/./g'

to for example;

sed 's/.x*$/./g;s/.y*$/./g'

in the code above.

If you have two fasta files. Just insert one and change; if ($1 == 2) to if ($1 == 1) in the code, this way you only have to run it for one file.

This will print the names to 'mates.txt'. Only thing to do is to set your library name and insert sizes on the top of this file.

Bambus will probably generate a lot of errors, because some names are not found in the .contig file. But this shouldn't be a problem.

Hope this works otherwise ask me.