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Dhivya Arasappan

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Objectives

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Code Block
titleGet set up for the exercises
ls ../data
ls ../reference
 
#transcriptome
head ../reference/transcripts.fasta 
#see how many transcripts there are in the file
grep -c '^>' ../reference/transcripts.fasta
 
#genome
head ../reference/genome.fa
#see how many sequences there are in the file
grep -c '^>' ../reference/genome.fa
 
 
#annotation
head ../reference/genes.formatted.gtf
#see how many entries there are in this file
wc -l ../reference/genes.formatted.gtf

Load the module:Run BWA

Code Block
module load bwa

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NO NEED TO RUN THIS NOW- YOUR INDEX HAS ALREADY BEEN BUILT!

All the files starting with the prefix transcripts.fasta are your BWA index files.

Code Block
bwa index -a bwtsw reference/transcripts.fasta


Part 2. Align the samples to reference using bwa mem

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