10x genomics hashtag samples

Question

[HK]

Hello all,

I have 10x genomics single cell RNA sequencing data (fastq format) with hashtag also. I have

folder name: 50500822-SCS20-1 (This folder has 9 fastq files) 
    50500822-SCS20-1_S1_L001_R1_001.fastq 
    50500822-SCS20-1_S1_L001_R2_001.fastq 
    50500822-SCS20-1_S1_L001_I1_001.fastq 
    50500822-SCS20-1_S1_L002_R1_001.fastq 
    50500822-SCS20-1_S1_L002_R2_001.fastq 
    50500822-SCS20-1_S1_L002_I1_001.fastq
    50500822-SCS20-1_S1_L003_R1_001.fastq 
    50500822-SCS20-1_S1_L003_R2_001.fastq 
    50500822-SCS20-1_S1_L003_I1_001.fastq

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folder name: 50500822-SCS20-1-HT
50500822-SCS20-1-HT_S3_L001_R1_001.fastq
50500822-SCS20-1-HT_S3_L001_R2_001.fastq
50500822-SCS20-1-HT_S3_L001_I1_001.fastq
50500822-SCS20-1-HT_S3_L002_R1_001.fastq
50500822-SCS20-1-HT_S3_L002_R2_001.fastq
50500822-SCS20-1-HT_S3_L002_I1_001.fastq
50500822-SCS20-1-HT_S3_L003_R1_001.fastq
50500822-SCS20-1-HT_S3_L003_R2_001.fastq
50500822-SCS20-1-HT_S3_L003_I1_001.fastq

I have to do the alignment for this I am using cellRanger count. My questions are:

1. As I see different lanes (L001,L002,L003), should I first concatenate L001_R1, L002_R1 and L003_R1 (and also fo R2 on the same way) and then do the alignment.
2. How to handle the hastag in cellRanger. Or do I just simply align them as normal samples?

Answer 1

[swbarnes2]

If cellranger sees all the fastqs from different lanes together, it will handle that fine. No need to concatenate. In fact, should you do so and drop the lane part from the name, cellranger might not recognize the file names properly.

Answer 2

[HK]

Thanks for the reply. Can anyone help me with the hashtag thing. How to handle/analyze the sample with hashtag). So, what I understand is that the alignment is same for the samples with or without hashtags?