Commit 16dc4800 authored by yy1533's avatar yy1533
Browse files

📖 change to simple example as Bo Xia suggested

parent d79f32d1
......@@ -39,24 +39,19 @@ pip install ./
# Quick Start
Running `celseq2` pipeline is easy as 1-2-3, and here is a quick start tutorial
based on an example. Suppose user performed CEL-Seq2 and got samples sequenced
in the way shown as figure below.
based on an arbitrary example. Suppose user performed CEL-Seq2 and got samples
designed in the way shown as figure below.
The user had two biological samples with 8 and 96 cells respectively, which could come
from two time-points or two tissues. To reduce the batch effect as much as
possible, the user could possibly add different Illumina sequencing barcodes
to the two plates (shown as blue and orange dots), mix them and subsequently get
samples sequenced together but in three lanes (shown as red, green and purple
rectangles). Finally, the sequencer would generate totally 6 FASTQ reads files.
from two time-points, two tissues, or even two labs. Samples were marked with
two different Illumina sequencing barcodes (blue and orange dots), mixed
together, and subsequently sequenced in the same lane, which finally resulted
to 2 FASTQ files.
By running the pipeline of `celseq2`, the users would get two types of UMI count
- UMI count matrix per biological sample. Here 2 matrices in this example.
- UMI count matrix per lane per sample. Here 6 matrices in this example. This is
to allow assessment on reproducibility or possible batch effect.
By running the pipeline of `celseq2` with the them, the users would get
UMI count matrix for each of the two plates.
## Step-1: Define Experiment Table
......@@ -78,11 +73,7 @@ The content of experiment table in this example could be:
|----------------------- |--------------------- |------------------------- |------------------------- |
| wonderful_experiment1 | 1,8,2-7 | path/to/x-1-r1.fastq.gz | path/to/x-1-r2.fastq.gz |
| wonderful_experiment1 | 1-8 | path/to/x-3-r1.fastq.gz | path/to/x-3-r2.fastq.gz |
| wonderful_experiment1 | 8,7,6,5,4,3,2,1 | path/to/x-2-r1.fastq.gz | path/to/x-2-r2.fastq.gz |
| wonderful_experiment2 | 95-96,94-1,10 | path/to/y-2-r1.fastq.gz | path/to/y-2-r2.fastq.gz |
| wonderful_experiment2 | 1-96 | path/to/y-1-r1.fastq.gz | path/to/y-2-r2.fastq.gz |
| wonderful_experiment2 | 1-96 | path/to/y-3-r1.fastq.gz | path/to/y-3-r2.fastq.gz |
Each row records one pair of FASTQ reads.
......@@ -121,7 +112,7 @@ Run pipeline:
celseq2 --configfile /path/to/wonderful_CEL-Seq2_config.yaml
In addition, it is straightforward to run the pipeline of `celseq2` by
Alternatively, it is straightforward to run the pipeline of `celseq2` by
submitting jobs to cluster, as `celseq2` is built on top of `snakemake` which is
a powerful workflow management framework. For example, in login node on server,
user could run the following command to submit jobs to computing nodes. Here it
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