Job scripts

Index genome

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

Mapping

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

SAM to sorted BAM

samtools sort -o Aligned.out.sorted.bam Aligned.out.sam

Mapping evaluation

samtools flagstat Aligned.out.sorted.bam > flagstat.txt

Mapping evaluation results

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)

Outputs