I am running an AmpSeq data analysis using this paper (Fungicide Resistance and Host Influence on Population Structure in Botrytis spp. from Specialty Crops in California) as a guide.
I have joined reads 1 and 2 together using FastQ Joiner, trimmed the joined read, and now map the trimmed reads to BWA-MEM. I am wondering whether to use the joined reads as a paired-end or single-end on BWA-MEM.
Thanks
I have tried using it as a single read by inputting the trimmed read as a single file (single-end), and it worked. Also, I tried using the trimmed read and input file for paired-end; here, the same file was used as read 1 input and repeated as read 2 input, and it also worked.