ChIP-Seq analysis packages

Most of the packages are from ​Pepke et al., 2009 (Table 1)

ChIP-Seq Bake-Off results

To test:

• CisGenome
• ERANGE
• ​MACS (​README) (​Zhang et al., 2008)
• PeakSeq (did not tried because it can only use input from ELAND)
• SeqMonk
• ​SiSSRs(Inma tried this instead of PeakSeq)(​Reference) (​Manual)

Others:

• FindPeaks
• F-Seq
• GLITR
• QuEST
• SICER
• spp
• USeq
• Garrett's SOLEXA_ENRICHED_REGIONS.py code

Sample data for testing is from ​Marson et al, 2008, specifically ​GSE11724 from NCBI GEO, including these samples (mapped to the mm9 (July 2007) genome), with Bowtie output in the files /nfs/BaRC/ChIP_Seq_analysis/GSE11724/+.k3.best.map and mapped as shown in map_with_bowtie.sh and also described in Data_sources.txt What assembly are WIG files from the publication?

• GSM307140 (Nanog_mES_rep1)
• GSM307141 (Nanog_mES_rep2)
• GSM307147 (HEK4me3_mES_rep1)
• GSM307148 (HEK4me3_mES_rep2)
• GSM307149 (HEK4me3_mES_rep3)
• GSM307155 (WCE_mES_rep1)
• GSM307154 (WCE_mES_rep2)

Outputs to share (all using July 2007 (mm9) mouse assembly):

• Genome-wide BED or WIG file
• BED file of peaks (preferably with some sort of scoring metric(s))
• Visualized output in IGV
• Shell script of all executed commands (for reproducability)
• Comments about the application and description of the method, including things such as these Questions about ChIP-Seq methods