Question: DEXSeq : Preprocessing within R for Forward-Reverse Library
gravatar for ZheFrench
23 months ago by
ZheFrench10 wrote:

I'm treating RNA-SEQ with forward-reverse library.

In the doc part 2.5 you explained very well how to configure Strandedness using the python script and the -s reverse option..(as htseqcount...)

In part B of the tutorial,  Preprocessing within R , it's not clear to me how you configure that only using only R with summarizeOverlaps.

I read something GenomicAlignments: Inverting strand when counting using summarizeOverlaps about  preprocess.reads=invertStrand

But that was not clear to me ...

Here I take account of the strand, but finally I'm not sure that it's counting well what it should because I did not succeed to configure library type , could you comment ? Alternative would be to simply set ignore.strand=TRUE to count all reads .

Retrieve 6 Tissue Specific Bam  3 vs 3

bamlst = BamFileList( fls, index=character(), yieldSize=100000, obeyQname=TRUE )

print("SummarizeOverlaps ")
SE = summarizeOverlaps( exonicParts, bamlst, mode="Union", inter.feature=TRUE,singleEnd=FALSE, ignore.strand=FALSE,fragments=FALSE)

colData(SE)$condition =  c("Heart", "Heart", "Heart", "Brain", "Brain", "Brain" ),

data = DDEXSeqDataSetFromSE( SE, design= ~ sample + exon + condition:exon )
dexseq • 352 views
ADD COMMENTlink modified 23 months ago • written 23 months ago by ZheFrench10
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 234 users visited in the last hour