I am working with SRR867646 reads, which contains 10919266 sequences for R1 and 2177589 for R2, and in fact, I am not able to do an alignment.
I found another Biostars' post where Devon Ryan suggest using the "repair.sh" script from the BBMap toolkit. I ran the script, but it generates the "r1" and "r2 files empty, and "singletons" file contains the same number of sequences as R1+R2 (10919266+2177589=13096855). My question is, how should I handle that? Should I treat "singletons" files as the reads were single-end?
Thanks in advance.