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This exercise will align a human total RNA-seq dataset composed (by design) almost exclusively of that includes numerous reads that cross splice junctions.


  • The bwa mem alignment
    • the program's progress output (on standard error) is redirected to a log file (2>hs_rna.bwamem.log)
    • its alignment records (on standard output) is piped to the next step (conversion to BAM)
  • Conversion of bwa mem's SAM output to BAM format
    • recall that the -b option to samtools view says to output in BAM format
  • Sorting the BAM file
    • samtools sort takes the binary output from samtools view and writes a sorted BAM file.

Because the progress output is being redirected to a log file, we won't see anything until the command completes. Then you should have a human_rnaseq.sort.bam file and an hs_rna.bwamem.log logfile.