Body: <p>I'm using Cell ranger to perform alignment on scRNA-seq data. I have more than 20 fastq files for it.</p>
  <p>They are stored in folder <code>test/test_S1_L00XX_R1_001.fastq.gz</code></p>
  <p>The problem is that when lane number (XX) is higher than 10, it returns error <code>Invalid path/prefix combination</code>. However, when I rename it as following <code>test/test_S1_L0XX_R1_001.fastq.gz</code>, it seems to work.</p>
  <p>My question is that if I have 20 fastq files and I named their lane from <code>L001 to L0022</code>, will it proceed files with <code>L0010 to L0022</code>?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-05-13T14:57:30.000Z
Comments.Text: I've never seen lane numbers that are padded to 4 digits (`L####`), only 3 (`L###`). Why are your files padded to 4 digits?
Comments.UserDisplayName: Ram RS
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-05-13T17:53:32.010Z
Comments.Text: 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.
Comments.UserDisplayName: Cloudberry
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-05-13T19:12:00.657Z
Comments.Text: Please show the actual fastq file names. It is unclear from the information you have provided what happens for numbers over 9.
Comments.UserDisplayName: gringer
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-05-14T05:51:13.027Z
Comments.Text: @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?
Comments.UserDisplayName: Tien
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-05-14T19:31:05.363Z
Comments.Text: 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?
Comments.UserDisplayName: swbarnes2
Tags: <cellranger>
Title: Cellranger count for more than 20 fastq files
ThreadText: # Cellranger count for more than 20 fastq files
  
  (Asked by: username_0 on 2024-05-13)
  
  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`?
  
  **Tags:** cellranger
  
  > **Comments:**
  > **username_1**: I've never seen lane numbers that are padded to 4 digits (`L####`), only 3 (`L###`). Why are your files padded to 4 digits?  
  > **username_2**: 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.  
  > **username_3**: Please show the actual fastq file names. It is unclear from the information you have provided what happens for numbers over 9.  
  > **username_0**: @username_2 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?  
  > **username_4**: 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?  
  
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  ## 0 answers
  
  