Exploring RNA-Seq data from Illumina effort
Here is what Sam sent
The 12 samples will be used for RNAseq for genome annotation – numbers indicate desired sequencing priority. Juvenile and larval samples were from Hollie Putnam (see links below for more info). Other tissue was from a single, adult geoduck, collected by Brent & Steven on 20150811. Gonad Heart Ctenidia Juvenile OA exposure (super low) (EPI_115, EPI_116) Juvenile ambient exposure (ambient treatment) (EPI_123, EPI_124) Larvae day 0 (EPI_74, EPI_75) Larvae day 5 (EPI_99) Crystalline style Byssus gland Mantle Labial palps Juvenile OA exposure – low treatment (EPI_107, EPI_108)
http://owl.fish.washington.edu/nightingales/Geoduck_NovaSeq/170630_A00104_0125_BH2V37DMXX/Demux/FastqOutput/L001/NR021/NR021_S8_L001_R1_001.fastq.gz http://owl.fish.washington.edu/nightingales/Geoduck_NovaSeq/170630_A00104_0125_BH2V37DMXX/Demux/FastqOutput/L001/NR021/NR021_S8_L001_R2_001.fastq.gz http://owl.fish.washington.edu/nightingales/Geoduck_NovaSeq/170630_A00104_0125_BH2V37DMXX/Demux/FastqOutput/L002/NR021/NR021_S8_L002_R1_001.fastq.gz http://owl.fish.washington.edu/nightingales/Geoduck_NovaSeq/170630_A00104_0125_BH2V37DMXX/Demux/FastqOutput/L002/NR021/NR021_S8_L002_R2_001.fastq.gz
These seem to be same library (PE ???) split over two lanes.
NovaSeq run for all combined. The MP libraries have a 800 bp insert and the RNA Seq libraries have a 300bp insert so they were loaded in a 10:1 MP:RNA into the NovaSeq.
Will attempt Trinity with larval samples- maybe Hyak… Guidance… https://genefish.wordpress.com/?s=Trinity