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" <petros...@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 ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
