FastqToSam (Picard) syntax paired-end reads

Question

[esteban.peguero]

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?

[h.mon]

Yes, but this splitting of files is uncommon nowadays. This was common when files were often transferred by ftp, ad internet speed was slower.

[esteban.peguero]

Thanks for the reply. In this case, I need to use this syntax because I'm using picard on a third-party platform that only supports one FASTQ input port.

[GenoMax]

You could cat the pieces together to make two inputs. R1_001, R1_002 etc go to R1.fastq. Make sure you use the same order in both R1/R2 files.