I'm trying to align probe sequence of rat230_2 micoarray to the transcriptome of rattus with utmost 6 mismatch. first I've build the index file from the transcriptome with the following command:
then I've tried to align the probe sequence to the index file with following command:
./Aligning/soap -a ./Aligning/probes.fasta -D ./Aligning/transcriptom.fasta.index -o output.txt -v 6 -p 4 -r 2
but i got the following output in the command line:
length y < 0, skip anyway ...
and the percent of alignment is 0.
where is the problem?