Commit b944b52c authored by Yun YAN's avatar Yun YAN Committed by GitHub
Browse files

📖 write an experiment table for example shown in previous pipeline

parent 4d7ea51c
......@@ -44,13 +44,19 @@ Running `celseq2` pipeline is easy as 1-2-3, and here is a quick start tutorial
based on an arbitrary example. Suppose user performed CEL-Seq2 and got samples
designed in the way shown as figure below.
![experiment_2plates_1lane](http://i.imgur.com/Vi2cD6e.png)
![experiment-old-pipeline-visualize](https://i.imgur.com/9ZEOnUj.png)
The user had two biological samples with 8 and 96 cells respectively, which could come
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.
This was the visualization of the experiment design as shown as in the [sample sheet](https://github.com/yanailab/CEL-Seq-pipeline/blob/133912cd4ceb20af0c67627ab883dfce8b9668df/sample_sheet_example.txt)
in previous pipeline.
The user had two biological samples which could come
from two time-points, two tissues, or even two labs.
They were denoted as squares and circles, respectively.
Each sample had 9 cells for example.
Though they were marked with same Illumina sequencing barcodes and sequenced togerther,
user was able to distinguish the source of cells because each cell had its own cell barcode.
Cells with barcode 1-9 came from sample-1 and cells with barcode 10-18 came from sample-2.
By running the pipeline of `celseq2` with the them, the users would get
UMI count matrix for each of the two plates.
......@@ -88,22 +94,23 @@ Fill information into the generated experiment table file.
:warning: Note: each slot cannot contain any space.
The content of experiment table in this example could be:
The content of experiment table in this example is:
| SAMPLE_NAME | CELL_BARCODES_INDEX | R1 | R2 |
|----------------------- |--------------------- |------------------------- |------------------------- |
| wonderful_experiment1 | 1,8,2-7 | path/to/sampleX-lane2-R1.fastq.gz | path/to/sampleX-lane2-R2.fastq.gz |
| wonderful_experiment2 | 1-96 | path/to/sampleY-lane2-R1.fastq.gz | path/to/sampleY-lane2-R2.fastq.gz |
| wonderful_experiment1 | 1-9 | path/to/lane1-R1.fastq.gz | path/to/lane1-R2.fastq.gz |
| wonderful_experiment2 | 10-18 | path/to/lane1-R1.fastq.gz | path/to/lane1-R2.fastq.gz |
| wonderful_experiment1 | 1,9,2-7 | path/to/lane2-R1.fastq.gz | path/to/lane2-R2.fastq.gz |
| wonderful_experiment2 | 18-10 | path/to/lane2-R1.fastq.gz | path/to/lane2-R2.fastq.gz |
Each row records one pair of FASTQ reads.
To ease the pain of manually specifying `CELL_BARCODES_INDEX`, `celseq2`
recognizes human inputs in various way. Examples of specification of barcodes
indexed from 1 to 8 that present in experiment-1 are listed and are all allowed.
1. `1-8`: the most straightforward way.
2. `1,8,2-7` or `1,8,7-2`: combination of individual and range assignment.
3. `8,1,7-2,6`: redundancy is tolerant.
1. `1-9`: the most straightforward way.
2. `1,9,2-7` or `1,9,7-2`: combination of individual and range assignment.
3. `9,1,7-2,6`: redundancy is tolerant.
Read [Experiment Table Specification](https://gitlab.com/Puriney/celseq2/wikis/Examples) for further details when more complexed
experiment design happens.
......@@ -200,4 +207,4 @@ Alternatively, user can gzip FASTQ and perform SAM2BAM:
```
celseq2-slim --project-dir /path/to/result_dir -n
celseq2-slim --project-dir /path/to/result_dir
```
\ No newline at end of file
```
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