I'm using Cell ranger to perform alignment on scRNA-seq data. I have more than 20 fastq files for it.
They are stored in folder test/test_S1_L00XX_R1_001.fastq.gz
The problem is that when lane number (XX) is higher than 10, it returns error Invalid path/prefix combination
. However, when I rename it as following test/test_S1_L0XX_R1_001.fastq.gz
, it seems to work.
My question is that if I have 20 fastq files and I named their lane from L001 to L0022
, will it proceed files with L0010 to L0022
?
L####
), only 3 (L###
). Why are your files padded to 4 digits? $\endgroup$