...
cs2mbs ref.csfasta > ref.m.fasta
where
| Code Block |
|---|
ref. |
...
fasta : reference in base space |
...
ref. |
...
csfasta : reference in color space (for temporary purposes) |
...
ref.m. |
...
fasta : reference in mock base space |
2. Create bowtie indexes for the reference genome
bowtie-build ref.m.fasta refindex
where
| Code Block |
|---|
ref.m. |
...
fasta : reference in mock base |
...
space refindex : basename for bowtie indexes |
3. Convert the reads to mock base space
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. |
4. Convert the reads to fastq
fasta2fastq in.m.fasta in_QV.qual > in.m.fastq
where
| Code Block |
|---|
in.m. |
...
fasta : reads file in mock base space |
...
in_QV. |
...
qual : corresponding quality file |
...
in.m. |
...
fastq : output fastq file |
5. Align using bowtie
bowtie -q -n 3 --best --norc refindex in.m.fastq out
where refindex : base name for the bowtie index of the reference
| Code Block |
|---|
refindex : base name for the bowtie index of the reference in.m. |
...
fastq : input fastq |
...
file out : mapping output file \-q : indicates use of fastq file \-n 3 : mismatches allowed in seed ( \-v 3 can be used instead to indicate mismatches allowed in entire alignment) \--norc : do not report reverse complement matches -- best: make bowtie search till it find the best alignment (based on number of mismatches and quality values at mismatched positions) |