Computational protocol: Nuclear factor I revealed as family of promoter binding transcription activators

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Protocol publication

[…] Clustering and correlation analyses of mapped reads were performed using ChIP-peak and ChIP-cor tools available on the ChIP-Seq Analysis Server [,]. In vivo NFI sites were defined using the ChIP-peak tool and applying the following parameters: window width - 300 bp, vicinity range - 300 bp, peak threshold - 5 tags, count cut-off - 1 tag, repeat filtering-on. Correlation analyses were made using ChIP-cor tool and applying the following parameters: window width - 50 bp, count cut-off - 1, normalization - global. Galaxy tools were used to operate on the genomic intervals [,]. […]

Pipeline specifications

Software tools ChIP-Cor, Galaxy
Application ChIP-seq analysis
Organisms Homo sapiens