DNase FAIRE data:
The file GSM543311.sga has been generated by concatenating all the files available on GEO for this GSM entry.
Also, be aware that we could not acertain the nature of these data as the descriptions given in the article and those find in GEO do not match.
bam files were converted to sam using samtools v0.1.14, unmapped reads were discarded and sam files were converted back to bam using samtools v0.1.14. and to bed using bamToBed v2.12.0 (bedtools). Files were lifted over to hg19 genome assembly using UCSC LiftOver tool and SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.2).