- --outSAMtype BAM SortedByCoordinate \
- --runThreadN $(CORES) \
- --outSAMstrandField intronMotif \
- --genomeDir $(STAR_INDEX_DIR) \
- --readFilesCommand "gzip -dc" \
- --readFilesIn $(TOPHAT_FASTQ_ARGUMENT);
- ln $(SRX)_star/Aligned.sortedByCoord.out.bam $@ -s
+ --outSAMtype BAM SortedByCoordinate \
+ --runThreadN $(CORES) \
+ --outSAMstrandField intronMotif \
+ --genomeDir $(STAR_INDEX_DIR) \
+ --readFilesCommand "gzip -dc" \
+ --readFilesIn $(TOPHAT_FASTQ_ARGUMENT);
+ ln $(SRX)_star/Aligned.*.bam $@ -s