Per Steven’s request, mapped our Olympia oyster 2bRAD data.

Mapped to:

• pbjelly_sjw_01 assembly.

This was run on our Mox computing node.

Slurm script: 20180515_oly_2bRAD_bowtie2_mapping.sh

The script is far too long to paste here, due to the shear number of input files. However, here’s a snippet to show the command and options that were used:

/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 \
--threads 24 \
--no-unal \
--score-min L,16,1 \
--local \
-L 16 \
-S /gscratch/srlab/sam/outputs/20180515_oly_2bRAD_bowtie2_mapping/20180515_oly_2bRAD_bowtie2_mapping.sam \
-x /gscratch/srlab/sam/data/O_lurida/oly_genome_assemblies/20180515_oly_bowtie2_pbjelly_sjw_01_genome_index/pbjelly_sjw_01_ref \
-U 

See the linked Slurm script above for the entire thing.

RESULTS:

Output folder:

• 20180515_oly_2bRAD_bowtie2_mapping

SAM file (104GB)

• 20180515_oly_2bRAD_bowtie2_mapping.sam

Mapping summary:

20180515_oly_2bRAD_bowtie2_mapping$ cat slurm-180337.out 
729797535 reads; of these:
  729797535 (100.00%) were unpaired; of these:
    273989476 (37.54%) aligned 0 times
    310581308 (42.56%) aligned exactly 1 time
    145226751 (19.90%) aligned >1 times
62.46% overall alignment rate