Question: tximport of 3 tagged RNA-seq counts from Salmon for downstream analysis with DESeq2
0
gravatar for rbenel
4 months ago by
rbenel0
rbenel0 wrote:

Hi, 

A 3' tagged RNAseq method was used to sequence my data, I then used Salmon for mapping and quantification. My question is about using tximport for downstream DESeq2. In the tximport workflow it says, "we recommend to use the original counts, e.g. txi$counts as a counts matrix, e.g. providing to DESeqDataSetFromMatrix". As DESeqDataSetFromMatrix only takes integers, is rounding after txi$counts appropriate?  

txi <- tximport(files, type = "salmon", tx2gene = tx2gene, countsFromAbundance="no") 

cts <- txi$counts
cts <- round(cts)

dds <- DESeqDataSetFromMatrix(cts,
                               colData = MetaData,
                               design = ~ ID + ... )

 

Thanks! 

ADD COMMENTlink modified 4 months ago by Michael Love23k • written 4 months ago by rbenel0
Answer: tximport of 3 tagged RNA-seq counts from Salmon for downstream analysis with DES
1
gravatar for Michael Love
4 months ago by
Michael Love23k
United States
Michael Love23k wrote:

Yes that’s recommended for 3’ tagged counts.

ADD COMMENTlink written 4 months ago by Michael Love23k
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