Content Comparison

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cd $SCRATCH/my_rnaseq_course/bwa_mem_results

Exercise 5: Samtools flagstat again on bwa output

samtools flagstat C1_R1.mem.bam

Exercise 6: Count spliced sequences in BWA results

How many spliced sequences are there in one of the alignment files,  C1_R1.mem.bam?

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samtools view C1_R1.mem.bam| cut -f 6 | grep 'N' | wc -l

Exercise 76: How does a read with tophat spliced alignment look in the BWA results?

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