STAR \
--runMode genomeGenerate \
--genomeDir /export/galaxy-central/database/job_working_directory/000/8/dataset_11_files/genomeDir \
--genomeFastaFiles /export/galaxy-central/database/files/000/dataset_10.dat \
--sjdbGTFfile /export/galaxy-central/database/files/000/dataset_9.dat \
--sjdbOverhang 100 \
> genome-indexing.log.txt 2>&1
STAR \
--genomeDir /export/galaxy-central/database/job_working_directory/000/8/dataset_11_files/genomeDir \
--readFilesIn \
/export/galaxy-central/database/files/000/dataset_7.dat \
/export/galaxy-central/database/files/000/dataset_8.dat \
> mapping.log.txt 2>&1
samtools sort -o Aligned.out.sorted.bam Aligned.out.sam
samtools flagstat Aligned.out.sorted.bam > flagstat.txt
14836 + 0 in total (QC-passed reads + QC-failed reads)
936 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
14836 + 0 mapped (100.00% : N/A)
13900 + 0 paired in sequencing
6950 + 0 read1
6950 + 0 read2
13900 + 0 properly paired (100.00% : N/A)
13900 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)