Can I merge Hi-C fastq files from different lanes?

Question

[Winter]

Hey everyone,

I am not a bioinformatician by training but am currently learning and trying to develop this skillset starting with the assembly of a new genome, so I appreciate all the help in advance.

I am using the VGP genome assembly pipeline to guide my work (https://doi.org/10.1038/s41587-023-02100-3).

I was given HiFi reads from one individual + Hi-C data from pooled, unrelated individuals. I am now trying to use this data for scaffolding, starting with pre-processing the Hi-C data by mapping with BWA-MEM2 and then generating the initial contact maps.

The Hi-C data appears to come from two different lanes as I have two sets of forward reads and two sets of reverse reads. My question is: can I create one set of forward reads and one set of reverse reads (by simply concatenating the respective files) and then use these merged datasets for mapping with BWA-MEM2? Or do I need to analyze each lane independently and then merge the output data somewhere downstream in the analysis?

Thanks again!

Answer 1

[GenoMax]

If the data is a technical sequencing replicate i.e. the same pool of samples has run on two lanes then you can indeed merge the two lanes of data at some point during the analysis (e.g. after alignments as BAM files).

[Winter]

Awesome, thank you for the concise and straight-forward answer!