Inspect P. generosa genome for candidate genes. First step is to extract output data from kallisto:

link to abundance data

abundance_data<-read.table(file="https://github.com/ocattau/kallisto/blob/main/analyses/output_01/abundance.tsv")
head(abundance_data)

link to run info json file

link to index file

Next step is to get count data on the abundance.tsv file. Before that can happen, Grab our Geoduck Transcriptome off of Mox and blast it against swiss_prot to get gene IDs

slurm script

#!/bin/bash
## 10.29.21 blast p.generosa on MOX
#SBATCH --job-name=blasting_p.generosa_10.29.21
## Allocation Definition
#SBATCH --account=srlab
#SBATCH --partition=srlab
## Nodes
#SBATCH --nodes=1
## Walltime (days-hours:minutes:seconds format)
#SBATCH --time=05-00:00:00
## Memory per node
#SBATCH --mem=500G
##turn on e-mail notification
#SBATCH --mail-type=ALL
#SBATCH --mail-user=ocattau@uw.edu
## Specify the working directory for this job
#SBATCH --chdir=/gscratch/srlab/ocattau/p.generosa #home directory


/gscratch/srlab/programs/ncbi-blast-2.8.1+/bin/blastx \ #load ncbi blastx software
-query /gscratch/srlab/ocattau/p.generosa/Pgenerosa_transcriptome_v5.fasta \ #this is the query file, should be the geoduck transcriptome
-db /gscratch/srlab/blastdbs/ncbi-sp-v5_20210224/swissprot \ #blast databse, should always be this swissprot in order to get gene annotations
-out /gscratch/srlab/ocattau/p.generosa/Panopea-generosa-uniprot_blastx.tab \ #output file 
-evalue 1E-20 \
-num_threads 30 \ #number of threads is going to be +28
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6

Output file to comapir to kallisto output

link to P.generosa.tab