Update RNA and integration tutorials

liulab-dfci · Apr 12, 2020 · 23578b2 · 23578b2
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diff --git 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
@@ -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':**