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Old 08-10-2010, 10:54 PM   #1
Yushan Hsiao
Junior Member
Location: Taiwan

Join Date: Aug 2010
Posts: 6
Smile Soap2: the -w command doesn't work

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?

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