Question: Chip-Seq Data
gravatar for Giuseppe Petrosino
7.0 years ago by
Giuseppe Petrosino40 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
alignment bowtie • 847 views
ADD COMMENTlink modified 7.0 years ago by graham etherington (TSL)100 • written 7.0 years ago by Giuseppe Petrosino40
gravatar for graham etherington (TSL)
7.0 years ago by
graham etherington (TSL)100 wrote:
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: 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" <>
ADD COMMENTlink written 7.0 years ago by graham etherington (TSL)100
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