Six raw data files have been provided for all our further RNA-seq analysis:
cds cd my_rnaseq_course cp -r /corral-repl/utexas/BioITeam/rnaseq_course/bowtie_exercise . & cd bowtie_exercise |
Load the bowtie module
module load bowtie |
What version of bowtie was loaded?
|
Next, index the reference file. THIS IS ALREADY DONE! The command you need is:
bowtie2-build |
Try typing this alone in the terminal and figuring out what to do from the help.
The first argument is the reference FASTA. The second argument is the "base" file name to use for the created index files. It will create a bunch of files beginning bowtie/NC_012967.1*. |
Finally, map the reads! The command you need is:
bowtie2 |
Try reading the help to figure out how to run the command yourself. This command takes a while. This is longer than we want to run a job on the head node (especially when all of us are doing it at once).
So, you will want to submit the full job to the cluster like you learned in the introduction.
But first, try to figure out the command and start it in interactive mode. Remember these are paired-end reads. Use control-c
to stop the job once you are sure it is running without an immediate error! Then, submit your command that is working to the TACC queue.
Create a
|
Your final output file is in SAM format. It's just a text file, so you can peek at it and see what it's like inside. Two warnings though:
head
or grep
or using a viewer like IGV, which we will cover later.Still, you should recognize some of the information on a line in a SAM file from the input FASTQ, and some of the other information is relatively straightforward to understand, like the position where the read mapped. Give this a try:
head C1_R1.sam |