---
title: "Genome_vs_transcriptome"
output: html_document
date: "2024-06-13"
---

```{bash}
#make databases for isoseq transcriptome and the genome assembly
makeblastdb -in /home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/data/Mtros-hq_transcripts.fasta -dbtype nucl -out isoseq_db
makeblastdb -in /home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/data/ncbi_dataset/data/GCF_036588685.1/cds_from_genomic.fasta -dbtype nucl -out genome_db

#blast foot protein fasta against isoseq database
blastn -query /home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/data/foot_proteins.fasta -db isoseq_db -out results_isoseq.txt \
-evalue 1E-20 \
-num_threads 8 \
-max_target_seqs 1 \
-outfmt 6
#Adding sequences from FASTA; added 411251 sequences in 11.0021 seconds.

#blast foot protein fasta against genome database
blastn -query /home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/data/foot_proteins.fasta -db genome_db -out results_genome.txt \
-evalue 1E-20 \
-num_threads 8 \
-max_target_seqs 1 \
-outfmt 6
#Adding sequences from FASTA; added 53269 sequences in 1.55116 seconds.
```
```{bash}
#how many blast hits did we get for each

wc -l /home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/results_isoseq.txt
#239

wc -l /home/shared/8TB_HDD_02/graceleuchtenberger/Github/byssus-exp-analysis/results_genome.txt
#278
```