Ribozero Output

[Derek-C]

Hi all,

I have some rRNA which was filtered out of my total RNA sample using Ribopicker. My sequence data is paired ends. I was wondering if it was possible to have Ribopicker output the actual rRNA sequences which each pair of reads was matched to as opposed to just two files of paired end reads again? Or if thats not possible could someone suggest another way to go about retrieving the sequences which each pair of rRNA reads maps to? Thanks