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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?

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    $\begingroup$ I've never seen lane numbers that are padded to 4 digits (L####), only 3 (L###). Why are your files padded to 4 digits? $\endgroup$
    – Ram RS
    Commented May 13 at 14:57
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    $\begingroup$ Out of curiosity: which sequencer has 20+ lanes? If your files are, in fact, from more than one sequencing run, you should think of another way of combining them to avoid hidden batch effects. $\endgroup$
    – Cloudberry
    Commented May 13 at 17:53
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    $\begingroup$ Please show the actual fastq file names. It is unclear from the information you have provided what happens for numbers over 9. $\endgroup$
    – gringer
    Commented May 13 at 19:12
  • $\begingroup$ @Cloudberry Yeah they are actually from different channel (6 lanes per channel). I might perform alignment on each channel separately. But if I combine them into one folder and do alignment together, can I do it by rename the lane in range L001 to L0024? $\endgroup$
    – Tien
    Commented May 14 at 5:51
  • $\begingroup$ If they are the same library, they have to be processed together. What people are asking you is, are you sure you wouldn't have better success with L024, not L0024? $\endgroup$
    – swbarnes2
    Commented May 14 at 19:31

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