Commit 159ce15f authored by Ruqian Lyu's avatar Ruqian Lyu
Browse files

update read me to include the bulk support

parent d9e02897
Pipeline #6677 passed with stages
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......@@ -22,7 +22,6 @@ with `CB` tag, eg. from single-cell preprocessing pipeline (cellranger)
- VCF, variant call file that contains the list of informative SNPs
- barcodeFile, the list of cell barcodes of the sperm cells
## Outputs
* *.mtx
......@@ -57,11 +56,24 @@ with `CB` tag, eg. from single-cell preprocessing pipeline (cellranger)
-h --help show help
Examples
./sscocaller --threads 10 AAAGTAGCACGTCTCT-1.raw.bam AAAGTAGCACGTCTCT-1.raw.bam.dp3.alt.vcf.gz barcodeFile.tsv ./percell/ccsnp-
./sscocaller --threads 4 possorted_bam. SNPs.vcf.gz barcodeFile.tsv ./percell/ccsnp
```
### Run for a Bam of a single cell (bulk sample)
For cases where the DNA reads do not have a cell barocode tag (CB) and all the DNA reads are from one cell (Bulk sample), `sscocaller` can
still be applied:
1, Prepare a bulkBC.txt file in which only one dummy cell barcode "bulk" is listed. It means in the bulkBC.txt file, there is only
one row and it has the text "bulk".
2, Apply sscocaller as above :
```
./sscocaller --threads 10 bulk.bam SNPs.vcf.gz bulkBC.txt ./output/bulksample
```
## Setup/installation
......@@ -106,14 +118,13 @@ The static bianry can be simply downloaded which works for GNU/Linux type OS: `.
The static build was generated by using docker image docker://svirlyu/sscocaller_nsb adapted from https://github.com/brentp/hts-nim/blob/master/Dockerfile
```
/usr/local/bin/nsb -s ./src/sscocaller.nim -n sscocaller.nimble -o /mnt/src -- --d:release --threads:on
```
With docker image : `svirlyu/sscocaller_nsb` contains the required static libraries. A static binary build of
sscocaller is available as downloadable artifacts at gitlab repo: "https://gitlab.svi.edu.au/biocellgen-public/sscocaller"
A static binary build of `sscocaller` is available as downloadable artifacts at gitlab repo: "https://gitlab.svi.edu.au/biocellgen-public/sscocaller" or via
the `Releases` tab
## Downstream analysis in R
......
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