How to visualize bowtie output?

[caspase]

Hi there,

I am new to sequencing so this is maybe a naive question. I did a chip-seq, and used bowtie to align all the short reads to genome. Then I found bowtie output, instead of "chrXX, coordinates, ....", is the following:

gi|110640213|ref|NC_008253.1| 15978 .....

I tried findpeaks to convert it to bed and wig, however it still has the these accession numbers instead of the chromosomes and coordinates.

Can somebody kindly help me out of this ?

Thanks a lot!

Wei

[simonandrews]

There was a thread running about this for the last couple of days over in the bioinformatics section of this site:

http://seqanswers.com/forums/showthread.php?t=3090

[tujchl]

caspase:
gi|110640213|ref|NC_008253.1|would be your chromosome, and 15978 would be coordinates and if you want to see your chromosome at once. you would change your reference header like >gi|110640213|ref|NC_008253.1| to >chr1 and rebuild your index