ChIP-seq fastq.gz files

[mikew]

Hi,

I recently completed my first ChIP-seq experiment.
I received fast.gz files from the sequencing company.
Obviously I now need to analyze this data.
How can I convert this data to a file format compatible with the USCS genome browser such as BAM or BED?

Any suggestions for analysis other than needing a good bioinformatician?

[pallevillesen]

Nope - you just answered your own question

You need someone to unzip and map the reads (fastq) to a reference genome (hg19?) and give you the aligned reads (bam) - and format a bedfile for showing the bamfile on ucsc.

If this makes no sense at all or if you are unfamiliar with linux software such as samtools, bwa and bowtie - then call the bioinformatics department. What you are asking is a simple and trivial task.