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| title | Get set up for the exercises |
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cds
cd my_rnaseq_course
cp -r /corral-repl/utexas/BioITeam/rnaseq_course_2015/tophat_exercise . &
cp -r /corral-repl/utexas/BioITeam/rnaseq_course_2015/tophat_results . & #pregenerated tophat results
#Lets get pregenerated bwa results as well for doing comparisons
cp -r /corral-repl/utexas/BioITeam/rnaseq_course_2015/bwa_exercise/bwa_mem_results . &
cd cd day_1/tophat_exercise
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Due to the size of the data and length of run time, many of the programs have already been run for this exercise. We will submit some jobs, but because we cannot wait for it to complete, we will be looking through already generated results. You will then be parsing the output, finding answers, and visualizing results (in the directory tophat_results).
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#This could take a while, so may not be a good idea to run on the head node
samtools view accepted_hits.sorted.bam | cut -f 6 | grep 'N' | wc -l
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Exercise 4: Samtools flagstat
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| title | Back to the directory with BWA results |
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cd $SCRATCH/my_rnaseq_course/day_1/bwa_exercise/bwa_mem_results |
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#This could take a while, so may not be a good idea to run on the head node
samtools view C1_R1.mem.bam| cut -f 6 | grep 'N' | wc -l
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