Download


CSEM (ChIP-Seq multi-read allocation using E-M algorithm): multi-read allocation

Download CSEM.
Download Bowtie (work with CSEM).


MOSAiCS: MOdel-based one and two Sample Analysis and Inference for ChIP-Seq Data

Download R package 'mosaics' (package source) (windows binary).


Preprocessed bin-level mappability, GC content, and ambiguity score

Download hg18 (binsize = 200): mappability (multi-reads), mappability (uni-reads), GC content, ambiguity.
Download mm9 (binsize = 200): mappability (multi-reads), mappability (uni-reads), GC content, ambiguity.


Preprocessing scripts for R package 'mosaics'

Download scripts for preprocessing.


Mappability

Download codes to generate PeakSeq nucletide-level mappability (chr*b.out).
Download preprocessed nucleotide-level mappability for uni-reads (chr*b.out) for hg18 and mm9.

OR

Download preprocessed nucleotide-level mappability for uni-reads and multi-reads and GC and ambiguity files
hg18 (30mers), mm9 (30mers) .


GC content & ambiguity score

Download genome assembly FASTA files from UCSC genome browser.