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Old 02-05-2016, 04:53 PM   #1
Location: Toronto

Join Date: Dec 2015
Posts: 10
Default Processing basespace generated bam file in DESeq2

Hi experts,

I am new to R and am using DESeq2 to find out differentially expressed genes from aged and young brain sample.
I am using RNA-seq workflow: gene-level exploratory analysis and differential expression.
[ ]
they have given an example wherein they have uploaded .bam files using airway package and then created the count (from .bam file).

I have .bam file generated using illumina basespace, I was wondering how I can use it using DESeq2 pakage in R.

Any suggestions?

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Old 02-05-2016, 05:22 PM   #2
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Location: Montreal

Join Date: May 2013
Posts: 367

As input, the count-based statistical methods, such as DESeq2 (Love, Huber, and Anders 2014), edgeR (Robinson, McCarthy, and Smyth 2009), limma with the voom method (Law et al. 2014), DSS (H. Wu, Wang, and Wu 2013), EBSeq (Leng et al. 2013) and BaySeq (Hardcastle and Kelly 2010), expect input data as obtained, e.g., from RNA-seq or another high-throughput sequencing experiment, in the form of a matrix of integer values.
The following tools can be used generate count matrices, summarizeOverlaps (Lawrence et al. 2013), featureCounts (Liao, Smyth, and Shi 2014), or htseq-count (Anders, Pyl, and Huber 2015):
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