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cds
cd my_rnaseq_course
cd day_1_partB/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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samtools flagstat accepted_hits.sorted.bam |
Let's see how this compares to BWA genome mapping results...
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cd $SCRATCH/my_rnaseq_course/day_1_partB/bwa_exercise/bwa_mem_results_genome/ |
Exercise 5: Count spliced sequences in BWA results
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Use threading option efficiently (tophat -p <number of threads>)
- Split one data file into smaller chunks and run multiple instances of tophat. 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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