How to deal with the twice BS-seq data for the same sample?

Question

[younglin113]

Hello everyone, Recently, I am dealing with a batch of BS-seq based single-base resolution DNA methylation data. But I got into this trouble: for the same sample, since the sequencing depth was not enough in the first time, so we added another sequencing procedure. And now I want to analyze the methylation level of each CpG site with bismark software, it bothers me how to merge those two datasets together to evaluate the methylation for one single sample. Should I :

1. merge the fastq files for further alignment OR
2. align the fastq files separately with bismark, and merge the BAM/SAM then for bismark_methylation_extractor OR
3. align and extract both separately, but merge the bismark_methylation_extractor results. OR

some other wiser choices.

Does anyone got those problems once? Thank in advance for your help.