<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>

CC BY-SA 4.0
2024-05-13T14:57:30.000Z
I've never seen lane numbers that are padded to 4 digits (`L####`), only 3 (`L###`). Why are your files padded to 4 digits?
Ram RS
CC BY-SA 4.0
2024-05-13T17:53:32.010Z
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.
Cloudberry
CC BY-SA 4.0
2024-05-13T19:12:00.657Z
Please show the actual fastq file names. It is unclear from the information you have provided what happens for numbers over 9.
gringer
CC BY-SA 4.0
2024-05-14T05:51:13.027Z
@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?
Tien
CC BY-SA 4.0
2024-05-14T19:31:05.363Z
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?
swbarnes2
<cellranger>
Cellranger count for more than 20 fastq files
# 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**: @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?  
> **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

