|CSEM (ChIP-Seq multi-read allocation using E-M algorithm) is a multi-read allocation algorithm.
Multi-reads are the reads that map to multiple locations on the reference genome.
Most common analysis of ChIP-seq data relies on using only reads that map uniquely to relevant reference genome (uni-reads).
This can lead to the omission of up to 30 percent of alignable reads.
Chung et al. (2011) illustrated that incorporation of multi-reads significantly increases sequencing depths,
leads to detection of novel peaks that are not otherwise identifiable with uni-reads,
and improves detection of peaks in low mappable regions.
The computational and experimental results established that multi-reads can be of critical importance
for studying DNA-protein interactions in highly repetitive regions of genomes with ChIP-seq experiments.
Output from CSEM can be used with other peak callers such as MOSAiCS and MACS
to identify peaks that are in both high and low mappable regions of genomes.
Please cite: Chung D, Kuan PF, Li B, SanalKumar R, Liang K, Bresnick E, Dewey C, and Keles S (2011),
"Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data,"
PLoS Computational Biology, 7(7): e1002111.
Please contact Dongjun Chung (firstname.lastname@example.org) if you have any questions or comments about this tool!
hg clone https://toolshed.g2.bx.psu.edu/repos/dongjun/csem
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