From M. musculus (July 2007 NCBI37/mm9).

ChIP-seq data:

	File name	Description	Feature	GEO-ID
1	BMAL1_ZT02_ChIP-Seq_rep1.sga	BMAL1 ZT02 rep1	BMAL1	GSM654880
2	BMAL1_ZT02_ChIP-Seq_rep2.sga	BMAL1 ZT02 rep2	BMAL1	GSM654881
3	BMAL1_ZT06_ChIP-Seq_rep1.sga	BMAL1 ZT06 rep1	BMAL1	GSM654882
4	BMAL1_ZT06_ChIP-Seq_rep2.sga	BMAL1 ZT06 rep2	BMAL1	GSM654883
5	BMAL1_ZT10_ChIP-Seq_rep1.sga	BMAL1 ZT10 rep1	BMAL1	GSM654884
6	BMAL1_ZT10_ChIP-Seq_rep2.sga	BMAL1 ZT10 rep2	BMAL1	GSM654885
7	BMAL1_ZT14_ChIP-Seq_rep1.sga	BMAL1 ZT14 rep1	BMAL1	GSM654886
8	BMAL1_ZT14_ChIP-Seq_rep2.sga	BMAL1 ZT14 rep2	BMAL1	GSM654887
9	BMAL1_ZT18_ChIP-Seq_rep1.sga	BMAL1 ZT18 rep1	BMAL1	GSM654888
10	BMAL1_ZT18_ChIP-Seq_rep2.sga	BMAL1 ZT18 rep2	BMAL1	GSM654889
11	BMAL1_ZT22_ChIP-Seq_rep1.sga	BMAL1 ZT22 rep1	BMAL1	GSM654890
12	BMAL1_ZT22_ChIP-Seq_rep2.sga	BMAL1 ZT22 rep2	BMAL1	GSM654891
13	Input_DNA.sga	Input DNA	Input	GSM654892

Technical Notes:

SRA files were downloaded from GEO, GEOID: GSE26602, and processed using the following bash commands:

1. Extract FASTQ from SRA file:
   

   fastq-dump SAMPLE.sra
   

2. Map reads to genome using Bowtie:
   

   bowtie --best --strata -m1 --sam -l 36 -n 3 h_sapiens_ncbi36 -q SAMPLE.fastq > SAMPLE.sam
   

3. Clean the results from unmapped reads:
   

   awk 'BEGIN {FS="\t"} $3 != "\*" {print $0}' SAMPLE.sam > SAMPLE_clean.sam
   

4. Make BAM file (using SamTools):
   

   samtools view -bS -o SAMPLE.bam SAMPLE_clean.sam
   

5. Sort it:
   

   samtools sort SAMPLE.bam SAMPLE_sorted
   

6. Make BED file:
   

   bamToBed -i SAMPLE_sorted.bam > SAMPLE.bed
   

7. Make SGA file (using ChIP-seq):
   

   bed2sga.pl -s hg18 -f FEATURE < SAMPLE.bed | sort -s -k1,1 -k3,3n -k4,4 | compactsga > SAMPLE.sga
   

References:

Rey G, Cesbron F, Rougemont J, Reinke H et al. Genome-wide and phase-specific DNA-binding rhythms of BMAL1 control circadian output functions in mouse liver. PLoS Biol 2011 Feb;9(2):e1000595. PMID: 21364973