Giuseppe, 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: http://liulab.dfci.harvard.edu/MACS/README.html Hope this helps, Graham

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

On 29/11/2011 15:16, "Giuseppe Petrosino" petrosino@ceinge.unina.it wrote:

Hi,I have illumina ChipSeq data in txt format with this structure:

@HWI-EAS225:8:1:1:58#0/1 NAGAGTGCCCGGGTTCAGTTCTCAGCACCCATGTGG +HWI-EAS225:8:1:1:58#0/1 DMSSSSSSUSSTTTUTSSSSSSSSSRQRTTTSSSUS @HWI-EAS225:8:1:1:1803#0/1 NCCATGGGAAGAGCTGGGCAGGCGGGCCGAGCGAAG +HWI-EAS225:8:1:1:1803#0/1 DLSTTSKOUTRRTTSSSTTTTSRPNNTOJOTSSRTB @HWI-EAS225:8:1:1:1547#0/1 NAGGGAAAAGTGGGACTGGCACTTGCCTCTACCAGC +HWI-EAS225:8:1:1:1547#0/1 DLVVVTPTVVVVUVVWVVUVVUWVVVWWWWWWWVVV

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.

Giuseppe