Hi, all!
Sorry to bother, but I'd like to inquire about the single-cell data.
When I check the demultiplexed barcode information associated with the sequencing files, I observed that FASTQ files with the prefix "AS062-7" and "AS062-8" contain identical samples. According to the methodological details in the paper, these represent two independent technical replicates per pool.
Upon further inspection of one replicate (e.g., "AS062-8"), I found that** multiple paired-end sequencing file pairs** sharing the same prefix which contains same samples, such as "ALAW-80428-AS062-8-5GEX-**S8-L003**-R1(R2)-001.fastq.gz", "ALAW-80428-AS062-8-5GEX-**S9-L001**-R1(R2)-002.fastq.gz" and "ALAW-80428-AS062-8-5GEX-**S9-L004**-R1(R2)-003.fastq.gz".
What confuses me is that if I want to obtain the **complete result of a sample's single sequencing** for use in a gene typing tool based on single-cell RNA-seq data, should I:
Split the sequences according to the barcode from **any single pair** of FASTQ files (e.g., S8_L003),** or **
**Extract and merge** target-sample sequences from **all three file pairs with the "AS062-8"** prefix?
Thank you for your attention!
Best regards,
Lynn
Created by Linlin Chen Chloe_Lynn Thank you for your answer! Following your guidance, I will pick one of the two replicates, merge all its lanes' FASTQ files, and then split them into different samples. Dear Lynn,
What you see is the same cells and the corresponding libraries that were split between different lanes before sequencing. If I understood your question correctly, you need to do the second option, where you extract and merge target-sample sequences from all three file pairs.
Kind regards,
Marina