Your ChipSeq data is already in fastq format. It appears to have Illunima
quality scores, so you'll need to use the NGS:QC and manipulation > FASTQ
Groomer tool, using 'Illumina 1.3+' as input and 'Sanger' quality format
as output.
As to using MACS, I've never used it before but you should be able to get
your answers by reading the manual at:
Hope this helps,

Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
Tel: +44 (0)1603 450601

On 29/11/2011 15:16, "Giuseppe Petrosino" <>

>Hi,I have illumina ChipSeq data in txt format with this structure:
>Can I convert into Fastq format?If so, how can I?
>Furthermore, after using Map with Bowtie for Illumina, how can I use MACS
>(Model-based Analysis of ChIP-Seq) if I have two files for IP samples and
>two files for Control samples?
>Thank you so much.

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