...
cs2mbs -d -r in.csfasta > in.m.fasta
where
| Code Block |
|---|
in. |
...
csfasta : reads file in color space |
...
in.m. |
...
fasta : reads file in mock base space |
...
\-d : drop the first colorspace base during conversion. This will ignore the first color space base which is part of the primer.
\-r : For each read, include the reverse of the mock base space sequence.
|
3. Create SOAP indexes for the reference genome
2bwt-builder ref.m.fasta
where
| Code Block |
|---|
ref.m. |
...
fasta : reference in mock base space |
4. Align using SOAP
soap -D ref.m.fasta.index -v 3 -a in.m.fasta -o out
where
| Code Block |
|---|
ref.m.fasta. |
...
index : base name for the SOAP reference indexes |
...
in.m. |
...
fasta : reads file (in mock base space) |
...
out : mapping output file
\-v 3 : mismatches allowed in the entire alignment
|
Troubleshooting
- If you have lots of warning message as 'length y < 0, countinue as 13', it means that your read length is too short, so SOAP cannot handle them properly. Currently, SOAP supports only reads longer than 30 bp.( NewsGroup article; it described 2.18 version, but 2.20 shows the same result.)