[BioC] DEseq for chip-seq data normalisation

Giuseppe Gallone giuseppe.gallone at dpag.ox.ac.uk
Mon Nov 4 17:47:25 CET 2013


I would like to use DEseq or DEseq2 to normalise the peak signal for 
some Chip-seq data across 10 biological replicates.

I started looking at the DEseq documentation - it seems the program 
requires a matrix arrangement of raw count data, where each row is a 
peak and each column is a replicate.

What is the best way to obtain this? I have bam files for the reads, 
obtained with BWA, and bed files (or alternatively narrowPeak files) for 
the peak intervals, obtained using MACS.

I gather it is possible to use a program called HTseq to compute these 
counts, however this program seems unable to deal with bed files, only 
with gff files, and I'd prefer working directly with my beds if at all 
possible. Thank you.

Best regards

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