Skip to content

Commit

Permalink
Updated README
Browse files Browse the repository at this point in the history
  • Loading branch information
baraaorabi committed Nov 8, 2022
1 parent e8cdf3f commit dd657c4
Showing 1 changed file with 15 additions and 7 deletions.
22 changes: 15 additions & 7 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -4,16 +4,21 @@ scTagger matches barcodes of short- and long-reads of single-cell RNA-seq experi
## Installation


### Running with Snakemake
We provided a simple `Snakefile` alongside a `config.yaml` file that runs the three stages of scTagger as well as Cell Ranger (assumes Cell Ranger is in path).


### Running manually
scTagger has a single python file in the py directory containing different functions to match long-reads and short-reads barcodes.
scTagger has a single python script containing different functions to match long-reads and short-reads barcodes.

The hole pipeline contains three steps that you can run each part separately:
The whole pipeline contains three steps that you can run each part separately:

#### Extract long-reads segment
The first step of the scTagger pipeline is to extract a segment where the probability of seeing a barcode is more than in other places. To run this step, you can use the following command.
The first step of the scTagger pipeline is to extract a segment where the probability of seeing a barcode is more than in other places.
To run this step, you can use the following command.

```
py/scTagger.py extract_lr_bc -r "path/to/long/read/fastq" -o "path/to/output/file" -p "path/to/output/plots"
./scTagger.py extract_lr_bc -r "path/to/long/read/fastq" -o "path/to/output/file" -p "path/to/output/plots"
```

**Augments**
Expand Down Expand Up @@ -43,7 +48,7 @@ py/scTagger.py extract_lr_bc -r "path/to/long/read/fastq" -o "path/to/output/fil
The second step is to extract the top short-reads barcodes that cover most of the reads.

```
py/scTagger.py extract_top_sr_bc -i "path/to/bam/file" -o "path/to/output/file" -p "path/to/output/plot"
./scTagger.py extract_top_sr_bc -i "path/to/bam/file" -o "path/to/output/file" -p "path/to/output/plot"
```

**Arguments**
Expand All @@ -66,7 +71,7 @@ py/scTagger.py extract_top_sr_bc -i "path/to/bam/file" -o "path/to/output/file"
#### Match long-reads segment with short-reads barcode
The last step is to match long read segments with selected barcodes from short reads
```
py/scTagger.py match_trie -lr "path/to/output/extract/long-read/segment" -sr "path/to/output/extract/top/short-read" -o "path/to/output/file" -t "number of threads"
./scTagger.py match_trie -lr "path/to/output/extract/long-read/segment" -sr "path/to/output/extract/top/short-read" -o "path/to/output/file" -t "number of threads"
```

**Arguments**
Expand All @@ -91,8 +96,11 @@ py/scTagger.py match_trie -lr "path/to/output/extract/long-read/segment" -sr "pa
* Fourth column is the long-read segment, and the Fifth column is a list of all short-read barcodes with minimum edit distance
* A bar plot that shows the number of long reads by the minimum edit distance of their match barcode

## Citing scTaggger
scTagger was first accepted to RECOMB-seq 2022 and is now published by iScience:

*Ghazal Ebrahimi, Baraa Orabi, Meghan Robinson, Cedric Chauve, Ryan Flannigan, and Faraz Hach. "Fast and accurate matching of cellular barcodes across short-and long-reads of single-cell RNA-seq experiments." iScience (2022). DOI:[10.1016/j.isci.2022.104530](https://doi.org/10.1016/j.isci.2022.104530)*


Note: This is an active development branch.
Please check the [paper](https://github.com/vpc-ccg/scTagger/tree/paper) branch of this repository for the archived paper experiements and implementation.

0 comments on commit dd657c4

Please sign in to comment.