Valouev 2008, A high resolution nucleosome map.

In vivo positions of more than 44 million putative nucleosome cores in C.elegans using SOLiD (Applied Biosystems).

• Raw data was downloaded from: SRA
• Input file format: SRA
• Download date: n/a

From C. elegans (May 2008 WS190/ce6).

DNase FAIRE data:

	Filename	Description	Feature	GEO-ID
1	MNase_sample.sga	MNase sample	MNase	-

FASTQ files were extracted from SRA files (ID SRR015241 and SRR015242) using fastq-dump (SRA toolkit v2.5.0) and mapped to the genome using Bowtie v0.12.8. SAM files were then converted into bam using samtools v0.1.14 and to bed using bamToBed v2.12.0 (bedtools). SGA conversion was carried out using bed2sga.pl (ChIP-Seq v. 1.5.3).

• Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM
  A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res. 2008 Jul;18(7):1051-63. doi: 10.1101/gr.076463.108. Epub 2008 May 13. 18477713