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footprinting

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Detect transcription factor binding footprints in ATAC-seq using TOBIAS, HINT-ATAC, Wellington, or scprinter. Use when identifying bound TF sites within accessible regions, correcting Tn5 insertion bias before footprinting, choosing between cleavage-based and aggregate-based footprinters, or comparing differential TF activity between conditions.

When to use

• identifying bound TF sites within accessible regions
• correcting Tn5 insertion bias before footprinting
• choosing between cleavage-based and aggregate-based footprinters
• comparing differential TF activity between conditions
• detecting short DNA stretches of reduced Tn5 cleavage
• per-base footprint scoring
• motif-anchored detection

When not to use

• tasks not stated in the skill text

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