Prepare for Day 2
To prepare for Day 2, try to start either BWA or Bowtie2 mapping of these two fastq files:
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$BI/ngs_course/human_variation/allseqs_R1.fastq
$BI/ngs_course/human_variation/allseqs_R2.fastq
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against this reference:
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$BI/ngs_course/human_variation/ref/hs37d5.fa
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followed by converting the output to bam format, sorting the bam file, and indexing the output.
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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 samtools. |
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| title | Submit to the TACC queue |
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| Move into your scratch directory and create a new directory: | Code Block |
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cds
mkdir day2
cd day2
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Then create a commands file with the commands below and use launcher_creator.py followed by qsub to run them. |
- Mapping
- For BWA, the commands are:
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| title | ONE LINE command for ALL bwa operations |
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module load bwa; bwa aln $BI/ngs_course/human_variation/ref/hs37d5.fa $BI/ngs_course/human_variation/allseqs_R1.fastq > r1.sai && bwa aln $BI/ngs_course/human_variation/ref/hs37d5.fa $BI/ngs_course/human_variation/allseqs_R2.fastq > r2.sai && bwa sampe $BI/ngs_course/human_variation/ref/hs37d5.fa r1.sai r2.sai $BI/ngs_course/human_variation/allseqs_R1.fastq $BI/ngs_course/human_variation/allseqs_R1.fastq > test.sam
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- For bowtie2:
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| title | One-line command for bowtie |
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module load bowtie/2.0.0b6; bowtie2 -t -x $BI/ngs_course/human_variation/ref/hs37d5_bowtie2 -1 $BI/ngs_course/human_variation/allseqs_R1.fastq -2 $BI/ngs_course/human_variation/allseqs_R2.fastq -S test.sam
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- Convert, sort, and index output:
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| title | One-line command for samtools |
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samtools view -S -b test.sam > test.bam && samtools sort test.bam test.sorted && samtools index test.sorted.bam
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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!