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module load perl
module load bowtie/2.2.0
cd $SCRATCH/my_rnaseq_course/day_4b/mirbase
bowtie2-build hairpin_cDNA_hsa.fa hairpin_cDNA_hsa.fa |
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To run the alignment, we execute a command that is very similar to BWA or Tophat2, but with different syntax:
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cd $SCRATCH/my_rnaseq_course/day_4b
bowtie2 --local -N 1 -L 16 -x mirbase/hairpin_cDNA_hsa.fa -U human_mirnaseq.fastq.gz -S human_mirnaseq.sam |
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cd $SCRATCH/my_rnaseq_course/day_4b
cp -r /corral-repl/utexas/BioITeam/rnaseq_course_2015/day_4b/PARalyzer_v1_5 .
cd PARalyzer_v1_5
ls -la PARalyzer_v1_5 |
As you will see, this directory contains many files, including the PARalyzer executable itself. It also contains the SAM file that we will analyze. Go ahead and take a look at the SAM file using less. In particular, below is a sample read that contains the characteristic mutational signal that (in principle) indicates close proximity to a protein during crosslinking:
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