CSEM (ChIP-Seq multi-read allocation using Expectation-Maximization)


Feb 9, 2013   CSEM v2.4 is online now. Replaced the Fenwick tree like structure with a linear structure to speed up CSEM. Added user-friendly reminders if CSEM guesses that users forget to compile the codes. Added '--no-extending-reads' option to 'run-csem' to disable extending reads. Added '--tag-align' option to 'csem-generate-input' to support tagAlign format files as inputs for downstream ChIP-Seq peak callers.

Sept 20, 2012   CSEM v1.0 is online now. Extend reads to the average fragment length and use the midpoint instead of the left most genomic coordinatefor allocating multi-reads. Take SAM/BAM formatted files as input and generate BAM formatted outputs. Generate input files for downstream peak callers using CSEM's BAM formatted file. Generate wiggle plots for visualization. Provide a script to extract reads from eland files.


Bo Li (bli25 at berkeley dot edu)

Source Code



(last modified on Dec 16, 2014)