I have a question regarding merging FASTQ files from the same sample but different sequencing runs.
We generated cDNA libraries using the 10X v3 protocol but weren’t sure they had worked so initially sequenced only a small fraction of the library (10,000 reads/cell) using a NovaSeq.
Once this data came back, it was analysed by generating count matrix and using Seurat we confirmed that the data looked usable. The same library was then sequenced to the full sequencing depth that we would require for proper analysis (with the same company and a NovaSeq).
I now have two FASTQs files- one from the original shallow sequence and another from the new run.
I am now wondering how to combine the two FASTQs into one?
Would cellranger aggr be best or could I use the —lanes function in the cellranger count?