How to convert bowtie output to wig

[masylichu]

Hi~,
Does anyone have a conversion tool or program for bowtie output to .wig format?
I need to visualize my aligment data on ucsc.

[natstreet]

There is probably a shorter route to achieve this but I have been using a combination of bed tools and the Jim Kent source code. This assumes you have your output from bowtie as a bam file rather than native bowtie format. I do this

bam-->bed using bed tools
bed-->Bigwig using bedGraphToBigWig from the Jim Kent source code

If you need a wig file rather than a bigwig file you can use bigWigToWig as a final step.

You can clone the Jim Kent source code from

git clone git://genome-source.cse.ucsc.edu/kent.git

[masylichu]

There is probably a shorter route to achieve this but I have been using a combination of bed tools and the Jim Kent source code. This assumes you have your output from bowtie as a bam file rather than native bowtie format. I do this

bam-->bed using bed tools
bed-->Bigwig using bedGraphToBigWig from the Jim Kent source code

If you need a wig file rather than a bigwig file you can use bigWigToWig as a final step.

You can clone the Jim Kent source code from

git clone git://genome-source.cse.ucsc.edu/kent.git

you mean that the .sam file from bowtie alignment should be converted into bam, and then be converted into bed.
Every alignment should be corresponding to one line of the bed file.

which code of Kent's can I use to convert the above bed file to wig file?

[natstreet]

Yes, I mean first convert sam format output to bam - which is why I say assuming you have the output as bam.

As far as I know there is no direct bed--wig program from Jim Kent, which is why I suggested bed--bigwig--wig. Not direct, but it works. Maybe the wiggles program that comes with tophat would also work for sam-->wig

There is also this perl script that you could try.