Transcriptome Alignment – Olympia oyster Trinity transcriptome aligned to genome with Bowtie2

Progress on generating bedgraphs from our Olympia oyster transcriptome continues.

Transcriptome assembly with Trinity completed 20180919.

Next up, align transcriptome to Olympia oyster genome.

Alignment and creation of BAM files was done using Bowtie2 on our HPC Mox node.

SBATCH script file:

Alignment was done using the following version of the Olympia oyster genome assembly:


Output folder:

Sorted BAM file:

Sorted & indexed BAM file (for IGV):

Will get the sorted BAM file converted to a bedgraph for use in IGV.

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