Combine multiple fastq.gz files

Question

[Zitian]

I have the following fastq.gz files:

HLGL3DSXY_L001_R1.fastq.gz  
HLGL3DSXY_L002_R1.fastq.gz  
HLGL3DSXY_L004_R1.fastq.gz  
HLGL3DSXY_L003_R1.fastq.gz  
HVFLTDSXY_L002_R1.fastq.gz  
HVFLTDSXY_L003_R1.fastq.gz  
HVFLTDSXY_L004_R1.fastq.gz  
HVGCVDSXY_L003_R1.fastq.gz

My question is then in which order should I cat these files together into a big fastq.gz file? Should I combine the lanes together (resulting in one file for each of the L001, L002, L003, and L004, respectively) and then cat these files together? or should I combine L001-004 for each run together first? Thanks

Answer 1

[GenoMax]

See my answer here: Concatenating fastq.gz files across lanes