bowtie, how to convert fastq into sam?

[fresh-potato]

NOW I have a chiq-seq raw data which is fastq format and need to be covert into sam file and finally I want to get a .wig file . I have got bowtie and samtools. Any one knows the command for bowtie to covert fastq into sam ?

[simonandrews]

Turning a fastq file into a sam file isn't really a conversion - it's an actual analysis step since you're having to map the data against a reference genome. You'll need to download a genome to map your data to - you can either get the fastq files for the genome you're using and use bowtie-build to index this, or you can get pre-indexed genomes for some of the more common assemblies from the bowtie web site.

Once you have your genome you'll need to construct a bowtie command to map your data to it. The exact command you use will depend to some extent on the nature of your data and what you're looking for - if you have long reads you might also want to look at bowtie2 which would be required if your alignments are likely to contain insertions or deletions relative to your genome sequence.

Below is an example bowtie command which is what we'd normally use to map our data.

bowtie -m 1 --strata --best --chunkmbs=512 --sam /path/to/indices input.fastq output.sam

This would give you a list of uniquely mapped reads in your genome. The -m 1 says only show reads which map exactly once, and the --strata --best say that if you have one alignment which is better than the rest (smaller number of mismatches) then you can report that even if there are other valid but poorer alignments. The --chunkmbs=512 is because on large genomes you can get huge numbers of alignments for some repeat sequences and the program runs out of assigned memory trying to decide which is 'best' and reports an error unless you give it some more memory to play with. Finally the --sam option writes the output in sam format so you don't need to do a conversion afterwards.