Question

Sorry about the bad heading, but the question was not easy to compress into one sentence…

I have two lists of contigs (list1 and list2). They contain mostly unique contigs, but with some overlap. I want to compare list1 and list2 and then create a list3 that contains all contigs in list1 minus those also present in list2. Is this possible with a simple cat/paste/grep/sort/uniq kind of batch command?

Thanks!

Answer 1

you can do it with sort and uniq :

sort list1 list2 list2 | uniq -u 

any lines in list2 will appear at least twice in the sorted output and so will be filtered by the uniq filter