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  • Soap2: the -w command doesn't work

    Problem:
    The maximum number of equal best hits command in Soap2 doesn't work.

    I'm now dealing with the small read alignment to map to the whole genome.
    I need to see all the coordinates of the multiple hit in each small read.
    The following is my command:
    ./soap -r 2 -a BD01.fas -D chr_all.fa.index -o output.txt

    The output shows that there will be a threshold of 10000 multiple hits.

    I found it on the website that Soap1 has the command to enlarge the maximum number of equal best hits. (./soap -w 99999)
    I've tried it, but it seems that it doens't work for Soap2.

    Is it possible to change the setting of it?

    Thanks!!

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