I have a collection of timmed fastq files from WES, each contain paired ends. Is it possible to map these files using bwa mem on galaxy?
Yes, bwa-mem can take a paired-end collection.
If read1 and read2 are in seperate fastq, then we specify each in the pair selection. For a fastq file contain both read1 and read2, how should the two reads be specified in the pair selection?
Select the same fastq in both?
Select "paired interleaved" under "single or paired-end reads" will do.