Lets compare the results of BWA (unspliced) and Hisat2 (spliced) by looking at the respective BAM files.
Exercise 5a: Examine a BAM/SAM file
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cds cd my_rnaseq_course/day_1_partB2 head bwa_exercise/bwa_mem_results_transcriptome/C1_R1.mem.sam #lot of these are header lines that start with @ grep -v '^@' bwa_exercise/bwa_mem_results_transcriptome/C1_R1.mem.sam|head |
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