I currently am using cutadapt on windows- thanks @emmaggie on Cutadapt On Windows for the help!
I was able to remove the adapter sequence of interest after one round of cutadapt, as seen in these pictures.
However, I am now left with a huge amount of blank reads- how do I get rid of them? Also, I seem to have had other overrepresented sequences taken away as well. Based on the images, should I be happy with that- were they probably adapters? Should I trim the other sequences away?
Thanks for any and all help!