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Hi all,
I was trying to align my short reads to reference genomes using different software and settings. I saw that some of them (for example "Mosaik") allow to set the hash lenght (4 - 32) while in others ("Soap", "Maq") it is not allowed to play with this parameter. I think that when the sequence length can be chosen, the software try to map the sequence to the reference genome using only the first bases of the short read (15, 17, 19 etc) that we set in the hash length..Is it correct? Which is the map strategy of the software where the hash length cannot be chosen? Do they use all the short read sequence for the mapping?
Thank
P
I was trying to align my short reads to reference genomes using different software and settings. I saw that some of them (for example "Mosaik") allow to set the hash lenght (4 - 32) while in others ("Soap", "Maq") it is not allowed to play with this parameter. I think that when the sequence length can be chosen, the software try to map the sequence to the reference genome using only the first bases of the short read (15, 17, 19 etc) that we set in the hash length..Is it correct? Which is the map strategy of the software where the hash length cannot be chosen? Do they use all the short read sequence for the mapping?
Thank
P