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samtools view C1_R1.mem.bam| awk '{if ($1 == 9) print}'

Help! I have a lots of reads and a large number of reads. Make tophat go faster!

• Use threading option efficiently (tophat -p <number of threads>)

• Split one data file into smaller chunks and run multiple instances of bwa. Finally concatenate the output.
  • WAIT! We have a pipeline for that!
  • Look for fastTophat in $BI/scripts  
    
• Split mapping by chromosome- mapping to each chromosome=1 job.

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