Add gene counts of same samples run on two lanes (Novaseq)

Question

[fakeeha]

Hello,

I am a beginner in the field of Bioinformatics and would like your feedback on a roadblock I am currently facing.

I have to perform DGE of RNAseq data using DESeq2 in R. For one fastq sample, I have 4 files - 2 forward and 2 reverse as the sample was run on two lanes (novaseq). I have 16 samples from each lane making it 32 samples overall. I did not merge the samples and performed FASTQC quality control, RNA star alignment and featureCounts separately. So, right now I have 2 mapped bam files and 2 featureCounts (gene counts) files. Before using DESeq2 , I want to confirm if I should add the gene counts for each sample.

I saw a post here which recommended using sumTechReps function from the edgeR package. However, I have biological replicates. I am not sure if it would be an appropriate choice. Please let me know if there are such functions that can add the gene counts for me or if you have any other recommendation, I would really appreciate that.

Thank you!

Answer 1

[swbarnes2]

You can combine the data from different lanes at any stage, fastqs, bams, counts.

Running the same sample in different lanes adds no significant technical artifacts.