A bug regarding input path of cellranger-count was fixed.

V1.1/SeuratAnalysis.R

@@ -100,6 +100,7 @@ rm(subsetted)
 DefaultAssay(samples.integrated)="RNA"	#See FAQ4 at https://satijalab.org/seurat/faq . Seurat suggests to use RNA data for DE tests and visualization.
 geneDescriptions=select(org.eg.db,keys=rownames(samples.integrated),columns='GENENAME',keytype='SYMBOL')%>%distinct(SYMBOL,.keep_all=T)
 colnames(geneDescriptions)[2]='name'
+geneDescriptions$name=gsub(',',';',geneDescriptions$name)
 if (reclustering)	#Reclustering using subsetted cells and renaming clusters (if cluster names are supplied).
 	samples.integrated=clusterCells(samples.integrated,nDim=nDims,assay='integrated',clusterIdents=clusterIdents)
 

V1.1/SeuratDE.R

@@ -74,6 +74,7 @@ initial.options=commandArgs(trailingOnly=F)
 source(file.path(dirname(sub("--file=","",initial.options[grep("--file=",initial.options)])),'DAseq.R'))
 options(future.globals.maxSize=2^32)
 load(sampleFile)
+geneDescriptions$name=gsub(',',';',geneDescriptions$name)
 DefaultAssay(samples.integrated)="RNA"
 if(dim(samples.integrated)[2]>10000) {
 	plotCells=sample(1:(dim(samples.integrated)[2]),10000)

V1.1/analysis_modules.sh

@@ -16,7 +16,7 @@ module load python/3.7.x-anaconda
 BLAST_MODULE=$SINGULARITY_FOLDER/ncbi/blast_2.11.0.sif
 #	CELLRANGER_MODULE=/work/CRI/zzhao/tools/Singularity/harvardinformatics/cellranger_3.1.0.simg
 CELLRANGER_MODULE=BioHPC_cellranger_4.0.0
-#module load cellranger/4.0.0	#Disabled because of a conflict with other modules. Enable it before use.
+module load cellranger/4.0.0	#Disabled because of a conflict with other modules. Enable it before use.
 CGATOOLS_MODULE=$SINGULARITY_FOLDER/sguthrie/cgatools_1.8.0.sif
 CUFFLINKS_MODULE=$SINGULARITY_FOLDER/robsyme/cufflinks_2.2.1.sif
 #DESEQ2_DEXSEQ_MODULE=$SINGULARITY_FOLDER/rticode/R_4.0.2_DESeq2_DEXSeq.sif
@@ -148,6 +148,7 @@ ENSEMBL_GENOME_GTF_HUMAN=$(echo $ENSEMBL_HUMAN_GENOME_PATH/*$ENSEMBL_VERSION.sor
 ENSEMBL_GENOME_GTF_HUMAN_CODING=$ENSEMBL_HUMAN_GENOME_PATH/Homo_sapiens.GRCh38.100.protein_coding.sorted.gtf
 ENSEMBL_GENOME_BIOMART_HUMAN_GENES=$ENSEMBL_HUMAN_GENOME_PATH/Homo_sapiens.GRCh38.100.genes.biomart
 ENSEMBL_GENOME_BIOMART_HUMAN_TRANSCRIPTS=$ENSEMBL_HUMAN_GENOME_PATH/Homo_sapiens.GRCh38.101.transcripts.biomart
+ENSEMBL_GENOME_BOWTIE2_INDEX_HUMAN=$ENSEMBL_HUMAN_GENOME_PATH/Bowtie2/genome
 #############################################################################################################################################
 ENSEMBL_MOUSE_GENOME_PATH=$REFERENCE_GENOMES/mouse/Ensembl/$ENSEMBL_VERSION
 ENSEMBL_GENOME_SEQ_MOUSE=$(echo $ENSEMBL_MOUSE_GENOME_PATH/*primary_assembly.fa)
@@ -157,6 +158,7 @@ ENSEMBL_GENOME_GTF_MOUSE=$(echo $ENSEMBL_MOUSE_GENOME_PATH/*$ENSEMBL_VERSION.sor
 ENSEMBL_GENOME_GTF_MOUSE_CODING=$ENSEMBL_MOUSE_GENOME_PATH/Mus_musculus.GRCm38.100.protein_coding.sorted.gtf
 ENSEMBL_GENOME_BIOMART_MOUSE_GENES=$ENSEMBL_MOUSE_GENOME_PATH/Mus_musculus.GRCm38.100.genes.biomart
 ENSEMBL_GENOME_BIOMART_MOUSE_TRANSCRIPTS=$ENSEMBL_MOUSE_GENOME_PATH/Mus_musculus.GRCm38.101.transcripts.biomart
+ENSEMBL_GENOME_BOWTIE2_INDEX_MOUSE=$ENSEMBL_MOUSE_GENOME_PATH/Bowtie2/genome
 ##############################################################################################################################################UCSC Reference files
 UCSC_COMMON_SNPS_HUMAN=$REFERENCE_GENOMES/human/UCSC/hg38/snp151Common.txt.ensembl
 UCSC_COMMON_SNPS_MOUSE=$REFERENCE_GENOMES/mouse/UCSC/mm10/snp142Common.txt.ensembl
@@ -181,6 +183,7 @@ human)
 	UCSC_COMMON_SNPS=$UCSC_COMMON_SNPS_HUMAN
 	ENSEMBL_UNIPROT_GENE_LOCATION=$ENSG_UNIPROT_LOCATION
 	ENSEMBL_UNIPROT_TRANSCRIPT_LOCATION=$ENST_UNIPROT_LOCATION
+	ENSEMBL_GENOME_BOWTIE2_INDEX=$ENSEMBL_GENOME_BOWTIE2_INDEX_HUMAN
 ;;
 mouse)
 	ENSEMBL_GENOME_PATH=$ENSEMBL_MOUSE_GENOME_PATH
@@ -194,6 +197,7 @@ mouse)
 	UCSC_COMMON_SNPS=$UCSC_COMMON_SNPS_MOUSE
 	ENSEMBL_UNIPROT_GENE_LOCATION=$ENSMUSG_UNIPROT_LOCATION
 	ENSEMBL_UNIPROT_TRANSCRIPT_LOCATION=$ENSMUST_UNIPROT_LOCATION
+	ENSEMBL_GENOME_BOWTIE2_INDEX=$ENSEMBL_GENOME_BOWTIE2_INDEX_MOUSE
 ;;
 esac
 #############################################################################################################################################

V1.1/scRNASeq_V1.1.log

 Date:
-Tue Apr 27 22:49:46 CDT 2021
+Mon May 24 13:58:42 CDT 2021
 
 Commands:
 
@@ -7,14 +7,14 @@ cd /work/CRI/zzhao/git/PipelineMaker/V1.4
 sh make_pipeline.sh V1.1 scRNASeq /work/CRI/zzhao/git "ngs/ngs_common.sh" "ngs/RNASeq/scRNASeq/ngs_*.sh ngs/RNASeq/scRNASeq/Seurat/ngs_*.sh ngs/ngs_open_igv.sh" "ngs/RNASeq/scRNASeq/ngs_cellranger_index.txt ngs/RNASeq/scRNASeq/*.csv ngs/RNASeq/scRNASeq/Seurat/Seurat.csv ngs/RNASeq/scRNASeq/Seurat/cc.genes.updated.2019.rdata ngs/RNASeq/scRNASeq/Seurat/*.R ngs/RNASeq/scRNASeq/my_variables.sh ngs/RNASeq/scRNASeq/scRNASeq_analysis.sh"
 
 Files:
--rwx------ 1 zzhao Morrison_lab 2682 Apr 27 11:17 ./system_common.sh
+-rwx------ 1 zzhao Morrison_lab 2681 May 24 13:58 ./system_common.sh
 -rwxr--r-- 1 zzhao Morrison_lab 2462 Dec  8 12:11 ./header.sh
--rwx------ 1 zzhao Morrison_lab 4708 Dec 18 09:48 ngs/ngs_common.sh
+-rwx------ 1 zzhao Morrison_lab 4994 Apr 28 10:07 ngs/ngs_common.sh
 -rw-r--r-- 1 zzhao Morrison_lab 2585 Nov 23 00:30 ngs/ngs_open_igv.sh
 -rw-r--r-- 1 zzhao Morrison_lab 8013 Jan 15 13:06 ngs/RNASeq/scRNASeq/ngs_cellranger.sh
 -rw-r--r-- 1 zzhao Morrison_lab 9630 Mar 31 23:32 ngs/RNASeq/scRNASeq/Seurat/ngs_seurat.sh
 -rwx------ 1 zzhao Morrison_lab 5790 Apr 15 14:57 ngs/RNASeq/scRNASeq/Seurat/ngs_sierra.sh
--rwxr--r-- 1 zzhao Morrison_lab 1928 Oct 27 10:19 ./footer.sh
+-rwxr--r-- 1 zzhao Morrison_lab 1928 Oct 27  2020 ./footer.sh
 -rwx------ 1 zzhao Morrison_lab 5160 Mar 11 20:55 ./run_analysis.sh
 -rw-r--r-- 1 zzhao Morrison_lab 7056 Apr 27 18:29 ./main.sh
 -rw-r--r-- 1 zzhao Morrison_lab 3704 Apr 27 22:48 ./help.sh
@@ -22,13 +22,13 @@ Files:
 -rw-r--r-- 1 zzhao Morrison_lab  1922 Jul 17  2020 ngs/RNASeq/scRNASeq/my_variables.sh
 -rw-r--r-- 1 zzhao Morrison_lab  4345 Mar 12  2020 ngs/RNASeq/scRNASeq/ngs_cellranger_index.txt
 -rw-r--r-- 1 zzhao Morrison_lab    68 Mar 12  2020 ngs/RNASeq/scRNASeq/Samples.csv
--rw-r--r-- 1 zzhao Morrison_lab 20831 Apr 27 22:43 ngs/RNASeq/scRNASeq/scRNASeq_analysis.sh
+-rw-r--r-- 1 zzhao Morrison_lab 20824 May 24 13:35 ngs/RNASeq/scRNASeq/scRNASeq_analysis.sh
 -rw-r--r-- 1 zzhao Morrison_lab  1000 Sep 25  2020 ngs/RNASeq/scRNASeq/Seurat/cc.genes.updated.2019.rdata
 -rw-r----- 1 zzhao Morrison_lab  8060 Mar 23 12:13 ngs/RNASeq/scRNASeq/Seurat/DAseqGetDAregion.R
 -rw-r--r-- 1 zzhao Morrison_lab  3262 Mar 26 18:22 ngs/RNASeq/scRNASeq/Seurat/DAseq.R
--rw-r--r-- 1 zzhao Morrison_lab  9753 Mar 30 09:34 ngs/RNASeq/scRNASeq/Seurat/SeuratAnalysis.R
+-rw-r--r-- 1 zzhao Morrison_lab  9811 Apr 28 22:30 ngs/RNASeq/scRNASeq/Seurat/SeuratAnalysis.R
 -rw-r--r-- 1 zzhao Morrison_lab   302 Jul 21  2020 ngs/RNASeq/scRNASeq/Seurat/Seurat.csv
--rw-r--r-- 1 zzhao Morrison_lab  7324 Mar 24 21:13 ngs/RNASeq/scRNASeq/Seurat/SeuratDE.R
+-rw-r--r-- 1 zzhao Morrison_lab  7382 Apr 28 22:29 ngs/RNASeq/scRNASeq/Seurat/SeuratDE.R
 -rw-r--r-- 1 zzhao Morrison_lab  6464 Jan 15 13:18 ngs/RNASeq/scRNASeq/Seurat/SeuratFiltering.R
 -rw-r--r-- 1 zzhao Morrison_lab  7528 Mar 29 14:17 ngs/RNASeq/scRNASeq/Seurat/SeuratIntegration.R
 -rw-r--r-- 1 zzhao Morrison_lab  6277 Mar 30 09:35 ngs/RNASeq/scRNASeq/Seurat/SeuratMonocle.R

V1.1/scRNASeq_analysis.sh

@@ -119,7 +119,7 @@ then
 	else
 		expID=$3
 	fi
-	sh $SCRIPT_FOLDER/run_analysis.sh per_sample $JOB_QUEUE "${STEP_OUTPUT_FOLDER[cellranger_mkfastq]}/$expID/H*BGX?/*" ${STEP_OUTPUT_FOLDER[cellranger_count]} cellranger_count $SPECIES $ANALYSIS_MODE "$4" "$5" "$6"
+	sh $SCRIPT_FOLDER/run_analysis.sh per_sample $JOB_QUEUE "${STEP_OUTPUT_FOLDER[cellranger_mkfastq]}/H*BGX?/*" ${STEP_OUTPUT_FOLDER[cellranger_count]} cellranger_count $SPECIES $ANALYSIS_MODE "$4" "$5" "$6"
 fi
 ######################################################
 if [ "$ANALYSIS_STEP" == "cellranger_count_merged" ]