Problem in alignment with soap

Question

[m_punisher6]

Hi all

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:

./Aligning/2bwt-builder ./Aligning/transcriptom.fasta

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?

thanks,

Mansoor,

[Benn]

I think you misuse "./"

You only need to use this for an execution file, e.g.:

./Aligning/2bwt-builder /Aligning/transcriptom.fasta

./Aligning/soap -a /Aligning/probes.fasta -D /Aligning/transcriptom.fasta.index -o output.txt -v 6 -p 4 -r 2

[m_punisher6]

yes you are right but the problem is still exist.

[Benn]

Are you sure soap works with FASTA instead of FASTQ?? I am not sure, I have never tried it.

Try to see if you get unmapped reads with -u option.

[m_punisher6]

Yes it is work. I found the problem. it doesn't work for read with length less than 27. so I used bwa aligner.