diff --git a/CTEHR-Training.md b/CTEHR-Training.md
index 366e4b1..0be3832 100644
--- a/CTEHR-Training.md
+++ b/CTEHR-Training.md
@@ -1,5 +1,5 @@
-#
 DMSO is the control group and TCDD is the treatment group. We will be using data related to only these groups. There are six samples in total. Ignore the rest. Sequencing data is from two lanes, and these have to be concatenated before processing.
+
 #1. Installation and Setup  
 ##20160310 Get the files
 Log in VPN  
@@ -7,12 +7,37 @@ Open terminal on mac
 Type `ssh -p 22 candice@nfsc-oracle.tamu.edu`  
 Type password  
 Under folder `Assignment`, exicute `git clone https://github.com/chapkinlab/sequencing-pipeline.git`  
-`wget ftp://ftp.ensembl.org/pub/release-79/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz`  
-`wget ftp://ftp.ensembl.org/pub/release-81/gtf/homo_sapiens/Homo_sapiens.GRCh38.81.gtf.gz`     
+`wget ftp://ftp.ensembl.org/pub/release-84/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz`  
+`wget ftp://ftp.ensembl.org/pub/release-84/gtf/homo_sapiens/Homo_sapiens.GRCh38.84.gtf.gz`     
 ##20160311
 To verify that the pipeline is installed and up-to-date, navigate to the `sequencing-pipeline` directory, and issue a `git pull`. An `Already up-to-date` message confirms the update.  
+
 #2. Obtaining Sequencing Datasets  
+`cp -r /mnt/nas/Organoid-data-04242014/FastqFile ./home/candice/Assignment/FastqFile`  
+
 #3. Quality Check  
+##20160312
+`mkdir FastqFiles_fastq`
+gunzip every fastq.gz files
+Create a experiment list in `Assignment/sequencing-pipeline/lists`: `vim candice_list`
+In `candice_list`:  
+species="grch38-human"  
+samplelist=(\  
+/home/candice/Assignment/FastqFile/Sample_DMSO1/DMSO1_AGTTCC_L001_R1_001.fastq.gz \  
+/home/candice/Assignment/FastqFile/Sample_DMSO1/DMSO1_AGTTCC_L002_R1_001.fastq.gz \  
+/home/candice/Assignment/FastqFile/Sample_DMSO2/DMSO2_GTGAAA_L001_R1_001.fastq.gz \  
+/home/candice/Assignment/FastqFile/Sample_DMSO2/DMSO2_GTGAAA_L002_R1_001.fastq.gz \  
+/home/candice/Assignment/FastqFile/Sample_DMSO3/DMSO3_TGACCA_L001_R1_001.fastq.gz \  
+/home/candice/Assignment/FastqFile/Sample_DMSO3/DMSO3_TGACCA_L002_R1_001.fastq.gz \  
+/home/candice/Assignment/FastqFile/Sample_TCDD1/TCDD1_CCGTCC_L001_R1_001.fastq.gz \  
+/home/candice/Assignment/FastqFile/Sample_TCDD1/TCDD1_CCGTCC_L002_R1_001.fastq.gz \  
+/home/candice/Assignment/FastqFile/Sample_TCDD2/TCDD2_CGATGT_L001_R1_001.fastq.gz \  
+/home/candice/Assignment/FastqFile/Sample_TCDD2/TCDD2_CGATGT_L002_R1_001.fastq.gz \  
+/home/candice/Assignment/FastqFile/Sample_TCDD3/TCDD3_CAGATC_L001_R1_001.fastq.gz \  
+/home/candice/Assignment/FastqFile/Sample_TCDD3/TCDD3_CAGATC_L002_R1_001.fastq.gz \
+)    
+From the sequencing pipeline directory, run `main-scripts/preqc.sh lists/candice_list`  
+
 #4. Dataset Pre processing and List files  
 `cd sequencing-pipeline/main-scripts`  
 `vi concat.sh`
@@ -20,4 +45,26 @@ modifying the cut commmand on [this line](https://github.com/chapkinlab/sequenci
 remove the # commenting character) [this line](https://github.com/chapkinlab/sequencing-pipeline/blob/3155b43c4877023fc7a6b5699b77dd42d9bc2389/main-scripts/concat.sh#L50) in your local copy of the concat.sh script and then run it.  
 `mkdir FastqFile_processed`  
 `./sequencing-pipeline/main-scripts/concat.sh ./FastqFile/ ./FastqFile_processed`   
+(sample list is optional)  
+
+#5. Mapping reads to the genome  
+Edit `candice_list`:  
+species="grch38-human"  
+samplelist=(\  
+/home/candice/Assignment/FastqFile_processed/DMSO1.fastq.bz2 \  
+/home/candice/Assignment/FastqFile_processed/DMSO2.fastq.bz2 \  
+/home/candice/Assignment/FastqFile_processed/DMSO3.fastq.bz2 \  
+/home/candice/Assignment/FastqFile_processed/TCDD1.fastq.bz2 \  
+/home/candice/Assignment/FastqFile_processed/TCDD2.fastq.bz2 \  
+/home/candice/Assignment/FastqFile_processed/TCDD3.fastq.bz2 \  
+)    
+mv Homo_sapiens.GRCh38.84.gtf.gz FastqFile_processed/  
+mv Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz FastqFile_processed/  
+gunzip Homo_sapiens.GRCh38.84.gtf.gz   
+gunzip Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz   
+cd ../sequencing-pipeline/
+main-scripts/map.sh lists/candice_list 2> err.log | tee out.log  
+
+#6. Analysis Summarization  
+#7. Gene Differential Expression Analysis