---
title: "06-Annot-novel"
output: html_document
date: "2025-08-05"
---

Annotating novel transcripts


```{bash}
cd /home/shared/16TB_HDD_01/blast_dbs/nt
/home/shared/ncbi-blast-2.15.0+/bin/update_blastdb.pl --decompress nt
```

Sam has nt database at 

/home/shared/8TB_HDD_01/sam/data/blastdbs/20240603-nt

```{bash}
/home/shared/ncbi-blast-2.15.0+/bin/blastn \
  -query ../output/04-align-v1/stringtie_out/transcripts.fa \
  -db /home/shared/8TB_HDD_01/sam/data/blastdbs/20240603-nt/nt \
  -out ../output/06-Annot-novel/trn_blastn_nt.tab \
  -outfmt 6 \
  -max_target_seqs 1 \
  -max_hsps 1 \
  -evalue 1e-5 \
  -num_threads 42 \
  -task megablast
```

```{bash}
head ../output/06-Annot-novel/trn_blastn_nt.tab
```



