Question: Reads with ambiguous annotation
0
gravatar for raya.fai
3 months ago by
raya.fai50
raya.fai50 wrote:

Hi,

We have a question about the proper handing of ambiguous annotation reads when using DESeq2. In our bacterial RNAseq data there is a fraction of reads (0.5-2%) that map inconclusively to two adjacent genes (gene A and gene B). We count such reads twice, one for gene A and one for gene B. Can we use DESeq2 for such counting? We prefer not to exclude these reads because they may have biological meaning.

Thank you very much, Raya

deseq2 • 79 views
ADD COMMENTlink modified 3 months ago by Michael Love26k • written 3 months ago by raya.fai50
Answer: Reads with ambiguous annotation
0
gravatar for Michael Love
3 months ago by
Michael Love26k
United States
Michael Love26k wrote:

You can use a method such as Salmon to perform quantification followed by tximport and DESeqDataSetFromTximport. This is our official pipeline for taking in the proportioned reads, and has been thoroughly benchmarked.

Additionally, we have a method Swish in the fishpond Bioconductor package which focuses on when there is substantial uncertainty in read assignment, as occurs in transcript level analysis or in gene level for scRNA-Seq.

ADD COMMENTlink modified 3 months ago • written 3 months ago by Michael Love26k

Thank you very much! Raya

ADD REPLYlink written 3 months ago by raya.fai50
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