Hello, I am new to this. I just did analysis by uploading three WT fastq files and three KO fastq files and created bam files, and then did DESeq2. Just to explain clearly, I call three WT files as WT1, WT2, WT3, and KO files as KO1, KO2 and KO3. WT1 and KO1 were sequenced at our first experiment, while WT2, WT3, KO2 and KO3 were sequenced at the 2nd experiment. Cells were sorted from naive mice…so we expect that there are no variations in cells used for RNA seq.
In PCA1 analysis, PC1 separates WT1 & KO1 from WT2, WT3, KO2 and KO3. I am wondering if there would be any method to mitigate the difference between this first and 2nd experiment reads. Any suggestion is welcome.
Welcome, @new
Yes, you could explore batch differences. See the bottom of the DESeq2 tool form for an example of how to organize the Factors/Factor levels.
We have tutorials here with more examples that include sample data + workflow templates. Start with the End-to-End section → Transcriptomics / Tutorial List
Hope this helps! 