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(a)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