==== ChIP-Seq analysis packages ====

Most of the packages are from
[[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Search&db=pubmed&term=19844228|Pepke et al., 2009]] (Table 1)

[[chipSeqBakeOff| ChIP-Seq Bake-Off results]]

To test:
  * CisGenome
  * ERANGE
  * [[http://liulab.dfci.harvard.edu/MACS/|MACS]] ([[http://liulab.dfci.harvard.edu/MACS/00README.html|README]]) ([[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Search&db=pubmed&term=18798982|Zhang et al., 2008]])
  * PeakSeq (did not tried because it can only use input from ELAND)
  * SeqMonk
  * [[http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/|SiSSRs]](Inma tried this instead of PeakSeq)([[http://nar.oxfordjournals.org/cgi/content/full/36/16/5221|Reference]]) ([[http://dir.nhlbi.nih.gov/papers/lmi/epigenomes/sissrs/SISSRs-Manual.pdf|Manual]]) 

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

Sample data for testing is from [[http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=Search&db=pubmed&term=18692474|Marson et al, 2008]], specifically [[http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11724|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]]