diff --git a/README.md b/README.md index 864180b..fcbb90a 100644 --- a/README.md +++ b/README.md @@ -841,7 +841,7 @@ Users also need to preprare for following files `CCDG_14151_B01_GRM_WGS_2020-08- ``` ${path}/src/Monopogen.py germline -a ${path}/apps -r region.lst \ - -p ./ \ + -p ./ -t 22 \ -g GRCh38.chr20.fa -m 3 -s all -o bm ``` This will take ~ 25 mins with output as @@ -1095,7 +1095,7 @@ Then, we need to collect single cell level read information by running the `cell ``` python ${path}/src/Monopogen.py somatic \ - -a ${path}/apps -r region.lst -t 50 \ + -a ${path}/apps -r region.lst -t 22 -w 10MB \ -i bm -l CB_7K.maester_scRNA.csv -s cellScan \ -g GRCh38.chr20.fa ``` @@ -1112,7 +1112,7 @@ Lines total/split/realigned/skipped: 1593789/42248/4781/0 Finally, we can run the LD refinment step to further improve the putative somatic SNV detection as (taking ~3 mins) ``` python ${path}/src/Monopogen.py somatic \ - -a ${path}/apps -r region.lst -t 50 \ + -a ${path}/apps -r region.lst -t 22 \ -i bm -l CB_7K.maester_scRNA.csv -s LDrefinement \ -g GRCh38.chr20.fa ```