I have RNA-seq data experiment which have done for some biological samples.
I need to do the gene expression quantification using these read files and after that differential gene expression analysis.
But RNA-seq data which I have is bit unusual in sense of experiment design. I'm wondering how much this can have effect on differential gene expression analysis results.
The problem with RNA-seq data is that for condition A, the reads are paired end and for condition B the reads are single end. Moreover for some biological replicates of condition D, it's single end and for some others replicate of it are paired paired end. All the data come from same lab and same sequencing platform.
I need to do DEG analysis A vs. B , A vs. C and C vs. B
Does anyone have idea how much this can effect on the result of expression level quantification and DEG analysis?
You don't say, but did they also use the same library prep protocol? If not, you're sunk.
One simple solution would be to use just single end reads i.e. discard the paired-data. For GEX (as opposed to transcript-level/isoform analysis) there is plenty of data to suggest that 1x50bp data is sufficient.