Analyzing Eland files from Solexa sequencing
Split the alignment results into individual files for each scaffold:
Count hits on each scaffold:
Portela J, Grunau C, Cosseau C, Beltran S, Dantec C, Parrinello H and Boissier, J. Whole-genome in-silico subtractive hybridization (WISH) - using massive sequencing for the identification of unique and repetitive sex-specific sequences: the example of Schistosoma mansoni. BMC Genomics - in press.