Versions Compared

Version Old Version 7 New Version 8
Changes made by

Dhivya Arasappan

Dhivya Arasappan

Saved on

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

Code Block
titleGet set up for the exercises
cds
cd my_rnaseq_course
cd day_1_partB/bwa_exercise

Run BWA

Load the module:

...

Part 2. Align the samples to reference using bwa mem

Alternatively, lets also try running  Running alignment using the newest and greatest, BWA MEM to the transcriptome. Alignment is just one single step with bwa mem.

 

Warning
titleSubmit to the TACC queue or run in an idev shell

Create a commands file and use launcher_creator.py followed by sbatch.

Code Block
titlePut this in your commands file
nano commands.mem
 
bwa mem reference/transcripts.fasta data/GSM794483_C1_R1_1.fq data/GSM794483_C1_R1_2.fq > C1_R1.mem.sam
bwa mem reference/transcripts.fasta data/GSM794484_C1_R2_1.fq data/GSM794484_C1_R2_2.fq > C1_R2.mem.sam 
bwa mem reference/transcripts.fasta data/GSM794485_C1_R3_1.fq data/GSM794485_C1_R3_2.fq > C1_R3.mem.sam 
bwa mem reference/transcripts.fasta data/GSM794486_C2_R1_1.fq data/GSM794486_C2_R1_2.fq > C2_R1.mem.sam 
bwa mem reference/transcripts.fasta data/GSM794487_C2_R2_1.fq data/GSM794487_C2_R2_2.fq > C2_R2.mem.sam 
bwa mem reference/transcripts.fasta data/GSM794488_C2_R3_1.fq data/GSM794488_C2_R3_2.fq > C2_R3.mem.sam
Expand
titleUse this Launcher_creator command

launcher_creator.py -n mem -t 04:00:00 -j commands.mem -q normal -a UT-2015-05-18 -m "module load bwa" -l bwa_mem_launcher.slurm

Since this will take a while to run, you can look at already generated results at: bwa_mem_results_transcriptome

Alternatively, we can also use bwa to make to the genome (reference/genome.fa). Those already generated results are at: bwa_mem_results_genome

 Help! I have a lots of reads and a large number of reads. Make BWA go faster!

  • Use threading option in the bwa command ( bwa -t <number of threads>)

  • Split one data file into smaller chunks and run multiple instances of bwa. Finally concatenate the output.
    • WAIT! We have a pipeline for that!
    • Look for runBWA.sh in $BI/bin  (it should be in your path)

Now that we are done mapping, lets look at how to assess mapping results.