How to use the short PE reads in the -R parameter

[ShuaishuaiTai]

Hi Malonge. When we used the short reads for the misassembly correction, the short reads usually have two files: *1.fq.gz and 2.fq.gz (PE sequencing), but the –R parameter only support one file in your manual (As of today, only one file is allowed, so please concatenate your data into one file if necessary). How to use the short PE reads in the -R parameter?

[malonge]

Hi there,

Paired-end info is not used to detect misassemblies - only coverage. So you can go ahead and just throw those reads into one large file. RagTag does allow one to specify a list of files that makes it a little more convenient.

There is a chance that I will revisit this in the future and try to use paired-end info to detect misassemblies.

Thanks