cellranger定量：One Library, Multiple Flowcells
If you have a library which was sequenced across multiple flowcells, you can pool the reads from both sequencing runs. Follow the steps in Running Multi-Library Samples to combine them in a single cellranger count run.
My FASTQs are not named like any of the above examples. It is likely that you received files that were processed through a proprietary LIMS system, which employs its own naming conventions.
10x pipelines need files named in the
demux convention in order to run properly. You will need to determine which file corresponds to which sample and which read type, likely by consulting your sequencing core or the individual who demultiplexed your flowcell.
It is highly likely that these files were initially processed with
bcl2fastq, so you will need to rename the files in the following format, once you track down their origin:
Read Type is one of:
I1: Sample index read (optional)
I2: Sample index read (optional)
R1: Read 1
R2: Read 2
After you have renamed those files into that format, you’ll use the following arguments:
SAMPLENAME from all lanes
SAMPLENAME from lane 1 only
│ ├── SRR12391722_1.fastq.gz
│ └── SRR12391722_2.fastq.gz
│ ├── SRR12391723_1.fastq.gz
│ └── SRR12391723_2.fastq.gz
│ ├── SRR12391724_1.fastq.gz
│ └── SRR12391724_2.fastq.gz
- nano 103.sh
- chmod +x 103.sh