Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
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bioinfouser2 ▴ 10
@bioinfouser2-15147
Last seen 19 months ago

Hello!

I have a really basic question!

In the DiffBind vignette, I have a question regarding the following texts:

If bFullLibrarySize is set to TRUE (default), then sizeFactors is called with the number of reads in the BAM/BED files for each ChIP sample, divided by the minimum of these; otherwise, estimateSizeFactors is invoked.

How does DiffBind internally calculates the number of reads of a BAM file to make those sizeFactors? In particular, which R package?

Thank you very much in advance!

DiffBind ChIP-seq • 203 views
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Rory Stark ★ 4.4k
@rory-stark-5741
Last seen 1 day ago
CRUK, Cambridge, UK

By default, dba.count() uses it's own internal C code to go through the .bam file. If the bUseSummarizeOverlaps=TRUE option is set, then the GenomicAlignments package is used.