Do you know what is the FastqToSam (Picard) syntax when using paired-end and the option "--USE_SEQUENTIAL_FASTQS"?
In the help section they provide an example:
"Use sequential fastq files with the suffix _###.fastq or _###.fastq.gz.The files should be named: _001., _002., ..., _XYZ. The base files should be: _001. An example would be: RUNNAME_S8_L005_R1_001.fastq RUNNAME_S8_L005_R1_002.fastq RUNNAME_S8_L005_R1_003.fastq RUNNAME_S8_L005_R1_004.fastq RUNNAME_S8_L005_R1_001.fastq should be provided as FASTQ."
I assume that in the case of paired-end it would be something like:
RUNNAME_S8_L005_R1_001.fastq RUNNAME_S8_L005_R2_001.fastq RUNNAME_S8_L005_R1_002.fastq RUNNAME_S8_L005_R2_002.fastq
would that be correct?