Schmidt 2012, CTCF binding evolution in mammals.


CTCF binding evolution by comparing ChIP-seq data from six mammals.



From M. mulatta (Nov 2015 BCM Mmul_8.0.1/rheMac8).

ChIP-seq data:

Filename Description Feature GEO-ID
1 ERS017357.sga liver|CTCF|rep1 CTCF -
2 ERS017348.sga liver|CTCF|rep2 CTCF -
3 ERS017376.sga liver|CTCF|rep3 CTCF -
4 ERS017353.sga liver|input|rep1 input -
5 ERS017367.sga liver|input|rep2 input -

Technical Notes

FASTQ files were mapped to the genome using Bowtie v1.1.1. SAM files were then converted to BAM using samtools v0.1.14 and to BED using bamToBed v2.27.0 (bedtools). BED to SGA conversion was carried out using bed2sga (ChIP-Seq v. 1.5.3).


Last update: 1 Oct 2018