Lecture 5

Set up directory and copy over files

Check out the first few lines from the GTF file

head gencode.v36.annotation.chr1.gtf | column -t -s $'\t' | less -S

Set up variables

module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 salmon/1.3.0 star/2.7.5a samtools/1.11 java/13.0.2 subread/2.0.1
BASE=/home/hgen_share
PICARD_JAR=$BASE/utils/picard.jar

Align with STAR

mkdir -p results
STAR --genomeDir $BASE/star/chr1 \
  --runThreadN 1 \
  --readFilesIn ex.fq \
  --outFileNamePrefix results/ex_ \
  --outSAMtype BAM SortedByCoordinate \
  --outSAMunmapped Within \
  --outSAMattributes Standard \
  --outFilterScoreMinOverLread 0.3 \
  --outFilterMatchNminOverLread 0.3 \
  --twopassMode Basic

Take a look at the summary statistics with less 

less results/ex_Log.final.out

Run featureCounts

featureCounts -T 4 -s 2 \
  -a gencode.v36.annotation.chr1.gtf \
  -o ex_featurecounts.txt \
  results/ex_Aligned.sortedByCoord.out.bam

Run Salmon

salmon quant -i $BASE/salmon/chr1 \
 -l A \
 -r ex.fq \
 -o ex_salmon \
 --seqBias

Download the output from the gene expression counters