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!
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