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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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