Prepare for Day 2
To prepare for Day 2, try to start either BWA or Bowtie2 mapping of these two fastq files:
against this reference:
followed by converting the output to bam format, sorting the bam file, and indexing the output.
For either BWA or Bowtie, you need an indexed reference generated by either
bwa index or
bowtie-build. Perhaps one already exists? You then call the alignment program(s)
bwa aln/bwa sampe or
bowtie. Conversion, sorting, and indexing of the output are all done via
Submit to the TACC queue
Move into your scratch directory and create a new directory:
Then create a
commands file with the commands below and use launcher_creator.py followed by qsub to run them.
- For BWA, the commands are:
- For bowtie2:
- Convert, sort, and index output:
For a bit of extra challenge, you could make two separate
commands files, one for each mapper, qsub them. Watch out - you'll need to make sure they both write output to different files, or run in different directories!