Question: DEseq2 with different fastq read numbers after salmon
1
gravatar for danalvoronov
8 months ago by
danalvoronov10
danalvoronov10 wrote:

Hi,

I am using DEseq2 to perform differential analysis of control and treated samples. However, I am not sure if DEseq takes into account number of initial reads in fastq files or number of aligned reads after salmon. Because I assume the greater the percentage of the reads are aligned, the greater the numReads is, does this get taken into account in DEseq2 or do I need to account for it myself before DEseq2?

Thank you,

Dan

deseq2 salmon salmon rna seq • 150 views
ADD COMMENTlink modified 8 months ago by Michael Love24k • written 8 months ago by danalvoronov10
Answer: DEseq2 with different fastq read numbers after salmon
0
gravatar for Michael Love
8 months ago by
Michael Love24k
United States
Michael Love24k wrote:

The Salmon => tximport => DESeq2 pipeline takes into account the library size, robustly estimated using the median ratio of estimated counts across all genes. So the total number of reads in the FASTQ or total number of mapped reads are not used to calculate size factors in DESeq2.

ADD COMMENTlink written 8 months ago by Michael Love24k
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