Small snippet that generates a genome index and aligns the RNAseq reads.

rnaseq/step3_align/snippet.sh

@@ -8,7 +8,7 @@ GENOME_INDEX="${STORAGE}/genome_index"
 mkdir -p "${GENOME_INDEX}"
 # Store the generated `Aligned.sortedByCoord.out.bam` in this dir.
 ALIGNMENT_OUTPUT="${STORAGE}/alignment"
-mkdir -p "${OUTPUT}"
+mkdir -p "${ALIGNMENT_OUTPUT}"
 
 # 1) Generate genome index.
 #
@@ -49,5 +49,5 @@ STAR \
     --readFilesCommand zcat \
     --readFilesIn "${R1}" "${R2}" \
     --outSAMtype BAM SortedByCoordinate \
+    --genomeDir ${GENOME_INDEX} \
     --outFileNamePrefix "${ALIGNMENT_OUTPUT}"
-