...
- Prepare target(DB) sequence.
Code Block $ bowtie-build <FASTA file> <DB name>
- Run bowtie. If you use fastq file (read sequences with quality scores),
If you want to ignore quality file, and use 'fasta' format reads,Code Block $ bowtie \-a \-q \-t \--suppress 6 <DB name> <Query fastq filename> <output filename>
Code Block $ bowtie \-a \-f \-t \--suppress 6 <DB name> <Query csfasta filename> <output filename>
bash script
I normally used the following bash script, after modifying each variable depending on data.
| Code Block |
|---|
#\!/bin/bash |
...
export BOWTIE_INDEXES="/home/taejoon/BOWTIE.idx/" |
...
BOWTIE="/home/taejoon/src64/bowtie/bowtie-0.12.5/bowtie" |
...
DB="DROME_E57_cdna_c" |
...
QUERY="SRR034220.called.fastq" |
...
OUT="SRR034220_called.$DB.bowtie_c" |
...
time $BOWTIE \-a \-C \-q \-t \--suppress 6 $DB $QUERY $OUT |
...
OUT="SRR034220_called.$DB.trim5_bowtie_c" |
...
time $BOWTIE \-a \-C \-q \-t \--trim5 5 \--trim3 5 \--suppress 6 $DB $QUERY $OUT |
Available on
User documentation
...