Objectives
In this lab, you will explore the mapping results generated previously. You will learn how to assess mapping results using samtools and unix commands. You will also look at the differences between mapping with BWA and mapping with Tophat2.
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# If using your own BWA mapped results (Sam files), they should be at: $SCRATCH/my_rnaseq_course/bwa_exercise # If not, you can get the results from: /corral-repl/utexas/BioITeam/rnaseq_course_2015/bwa_aln_results cds cd my_rnaseq_course cp -r /corral-repl/utexas/BioITeam/rnaseq_course_2015/bwa_aln_results . |
Samtools
Utilities for parsing and manipulating alignment files in SAM and BAM formats. It is useful for:
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samtools idxstats C1_R1.bam samtools idxstats C1_R1.mem.bam |
RNASEQC
A java program that generates rnaseq specific metrics for an input BAM file. Not available on TACC yet. Metrics like:
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