Deep Sequencing Notes
In our first run we encountered a problem with Eland, which was unable to align lane 5 and 7 due to the large number of reads we had in that lane.
The eland problem arises because the hashtable used in ELAND uses 24 bits (one bit less than defined in MAX_HASH_BITS), which means that Eland can only process 16'777'216 reads. One of our lanes had more, meaning that it crashed. The solution is to change
#define MAX_HASH_BITS 25to
#define MAX_HASH_BITS 26in the file ELAND_outer.h and the recompile the software.