Contains notes and custom scripts used to analyze Illumina reads for our NS-seq paper.
GCcontentInReads: contains script for calculating GC content in reads.
quadparsersuite: contains program for getting G4 location BED file, G4-CPMR, G4-start-site-CPMR, etc
See Methods and especially the Supp Methods to our paper, "Characterizing and controlling intrinsic biases of Lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins", for more information on analyzing peaks and reads. Get reads at the NCBI Short Read Archive (SRA): http://www.ncbi.nlm.nih.gov/sra
Search for: SRP045284
This should return the following 7 results:
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LexoG0 Reads (MCF7)- Rep1 1 ILLUMINA (Illumina HiSeq 2000) run: 162.1M spots, 8.1G bases, 5Gb downloads Accession: SRX669870 Select item 1239341
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NS-seq Reads (MCF7)- Rep 3 1 ILLUMINA (Illumina HiSeq 2000) run: 136.2M spots, 6.8G bases, 4.2Gb downloads Accession: SRX865372 Select item 1239340
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NS-seq Reads (MCF7)- Rep 2 1 ILLUMINA (Illumina HiSeq 2000) run: 139.3M spots, 7G bases, 4.2Gb downloads Accession: SRX865371 Select item 1239339
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LexoG0 Reads (MCF7) - Rep3 1 ILLUMINA (Illumina HiSeq 2000) run: 174.9M spots, 8.7G bases, 5.3Gb downloads Accession: SRX865370 Select item 1239338
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LexoG0 Reads (MCF7) - Rep2 1 ILLUMINA (Illumina HiSeq 2000) run: 196.5M spots, 9.8G bases, 6.1Gb downloads Accession: SRX865369 Select item 939888
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NS-seq Reads (MCF7)- Rep 1 1 ILLUMINA (Illumina HiSeq 2000) run: 128.2M spots, 6.4G bases, 3.8Gb downloads Accession: SRX669871 Select item 939886
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G0gDNA Control Reads (MCF7) 1 ILLUMINA (Illumina HiSeq 2000) run: 193.6M spots, 9.7G bases, 6.1Gb downloads Accession: SRX669869
Finding other data relevant to the paper:
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Gap locations in hg19
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CpG island locations in hg19
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human rDNA sequence