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DamID-seq pipeline

Brand Lab DamID-seq pipeline software

Owen Marshall, October 2014

Processing DamID-seq data involves extending single-end reads, aligning the reads to the genome and determining the coverage, similar to processing regular ChIP-seq datasets. However, as DamID data is represented as a log2 ratio of (Dam-fusion/Dam), normalisation of the sample and Dam-only control is necessary, and adding pseudocounts to mitigate the effect of background counts when represented as a ratio is highly recommended.

We use a single pipeline script to handle alignment, read extension, binned counts, normalisation, pseudocount addition and final ratio file generation. The script uses files in FASTQ or BAM as input, automatically detects sample names and the Dam-only control, and outputs the final log2 ratio files in GFF or bedGraph format.

The damidseq_pipeline software is available from github.  For file downloads, detailed usage and installation instructions, please to head to:

owenjm.github.io/damidseq_pipeline