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!!
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!!
