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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 sort bamfile sortedbamfile
samtools index sortedbamfile |
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#For bwa mem results
cp $SCRATCH/my_rnaseq_course/bwa_exercise/results/bwa_mem/C1_R1.mem.bam* .
# If not, you can get the results from:
/corral-repl/utexas/BioITeam/rnaseq_course_2015/bwa_mem_results
cds
cd my_rnaseq_course
cp -r /corral-repl/utexas/BioITeam/rnaseq_course_2015/bwa_mem_results . |
Exercise 3: Let's get some statistics: Samtools flagstat
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