Which internal tool does DiffBind uses to count BAM reads to calculate sizeFactor?
1
0
Entering edit mode
bioinfouser2 ▴ 10
@bioinfouser2-15147
Last seen 4.1 years 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 • 637 views
ADD COMMENT
0
Entering edit mode
Rory Stark ★ 5.2k
@rory-stark-5741
Last seen 10 days ago
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.

ADD COMMENT

Login before adding your answer.

Traffic: 964 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6