I have two paired end file sets for a sample.
Forward: sample_R1_001.fastq.gz, sample_R1_002.fastq.gz
Reverse sample_R2_001.fastq.gz, sample_R2_002.fastq.gz
This is not a multilane case. They were two separate runs from the same sample aliquot!!
- Should I concat R1_001 and R1_002 fastq files ?
- Or should I run them as two separate pipelines?
- Or should I run them separately till alignment and then do BAM merge like for multilane samples?