From 23578b2e45fd80cf4789eca2c09a7391d3062550 Mon Sep 17 00:00:00 2001 From: Dongqing Sun Date: Mon, 13 Apr 2020 01:56:02 +0800 Subject: [PATCH] Update RNA and integration tutorials --- example/Integration/Integration.md | 8 ++++---- example/RNA_infrastructure_10x/RNA_infrastructure_10x.md | 2 +- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/example/Integration/Integration.md b/example/Integration/Integration.md index dfe7ebd..0729e6f 100644 --- a/example/Integration/Integration.md +++ b/example/Integration/Integration.md @@ -13,8 +13,8 @@ $ conda activate MAESTRO ### Step 1. Configure the MAESTRO workflow Initialize the MAESTRO integration workflow using `MAESTRO scATAC-init` command. This will install a Snakefile and a config file in this directory. ```bash -$ MAESTRO integrate-init --rna-object /home1/wangchenfei/Project/SingleCell/scRNA/Analysis/MAESTRO_tutorial/10X_PBMC_8k_MAESTRO_V110/Result/Analysis/10X_PBMC_8k_scRNA_Object.rds \ ---atac-object /home1/wangchenfei/Project/SingleCell/scATAC/Analysis/MAESTRO_tutorial/10X_PBMC_10k_MAESTRO_V110/Result/Analysis/10X_PBMC_10k_scATAC_Object.rds \ +$ MAESTRO integrate-init --rna-object MAESTRO_tutorial/10X_PBMC_8k_MAESTRO_V110/Result/Analysis/10X_PBMC_8k_scRNA_Object.rds \ +--atac-object MAESTRO_tutorial/10X_PBMC_10k_MAESTRO_V110/Result/Analysis/10X_PBMC_10k_scATAC_Object.rds \ --directory 10X_PBMC_8kRNA_10kATAC_MAESTRO_V110 --outprefix 10X_PBMC_8kRNA_10kATAC ``` @@ -109,8 +109,8 @@ By default, MAESTRO will label the top 10 regulators using TF enrichment from GI cluster.2 = 0, type = "Integrated", SeuratObj = pbmc.RNA.res$RNA, - LISA.table = "/home1/wangchenfei/Project/SingleCell/scRNA/Analysis/MAESTRO_tutorial/10X_PBMC_8k_MAESTRO_V110/10X_PBMC_8k_lisa.txt", - GIGGLE.table = "/home1/wangchenfei/Project/SingleCell/scATAC/Analysis/MAESTRO_tutorial/10X_PBMC_10k_MAESTRO_V110/10X_PBMC_10k_giggle.txt", + LISA.table = "MAESTRO_tutorial/10X_PBMC_8k_MAESTRO_V110/10X_PBMC_8k_lisa.txt", + GIGGLE.table = "MAESTRO_tutorial/10X_PBMC_10k_MAESTRO_V110/10X_PBMC_10k_giggle.txt", visual.totalnumber = 100, name = "10X_PBMC_integrated_Monocyte_top") ``` diff --git a/example/RNA_infrastructure_10x/RNA_infrastructure_10x.md b/example/RNA_infrastructure_10x/RNA_infrastructure_10x.md index 5bfaf43..b33cdc5 100644 --- a/example/RNA_infrastructure_10x/RNA_infrastructure_10x.md +++ b/example/RNA_infrastructure_10x/RNA_infrastructure_10x.md @@ -83,7 +83,7 @@ Arguments | Description Arguments | Description --------- | ----------- `--mapindex` | Genome index directory for STAR. Users can just download the index file from [here](http://cistrome.org/~chenfei/MAESTRO/Refdata_scRNA_MAESTRO_GRCh38_1.1.0.tar.gz) and decompress it. Then specify the index directory for STAR, for example, `--mapindex Refdata_scRNA_MAESTRO_GRCh38_1.1.0/GRCh38_STAR_2.7.3a`. -`--rsem` | The prefix of transcript references for RSEM used by rsem-prepare-reference (Only required when the platform is Smartseq2). Users can directly download the reference file for [huamn](http://cistrome.org/~chenfei/MAESTRO/Refdata_scRNA_MAESTRO_GRCh38_1.1.0.tar.gz) and [mouse](http://cistrome.org/~chenfei/MAESTRO/Refdata_scRNA_MAESTRO_GRCm38_1.1.0.tar.gz) from CistromeDB and decompress them. Then specify the prefix for RSEM, for example, `--rsem Refdata_scRNA_MAESTRO_GRCh38_1.1.0/GRCh38_RSEM_1.3.2/GRCh38`. +`--rsem` | The prefix of transcript references for RSEM used by rsem-prepare-reference (Only required when the platform is Smartseq2). Users can directly download the reference file for [human](http://cistrome.org/~chenfei/MAESTRO/Refdata_scRNA_MAESTRO_GRCh38_1.1.0.tar.gz) and [mouse](http://cistrome.org/~chenfei/MAESTRO/Refdata_scRNA_MAESTRO_GRCm38_1.1.0.tar.gz) from CistromeDB and decompress them. Then specify the prefix for RSEM, for example, `--rsem Refdata_scRNA_MAESTRO_GRCh38_1.1.0/GRCh38_RSEM_1.3.2/GRCh38`. **Barcode arguments, for platform of 'Dropseq' or '10x-genomics':**