# Lab week 3

`mkdir labwk3` to make new folder for this week
`ls` to make sure the directory went to the right place

`cd /courses/bi278/Course_Materials/lab_03` to change directroies into this weeks lab folder
`ls` to see files

`cp P.bonniea_bbqs395.nanopore.fasta ~/labwk3` to copy into my directory for tis week
`cd ~`
`cd labwk3`
`ls` to make sure it was copied

to run prokka annotation
prokka --force --outdir ./bbqs395 --proteins/coursesbi278/Course_Materials/labwk3/Burkholderia_pseudomallei_K96 243_132.gbk --locustag BB395 --genus Paraburkholderia --species bonneia --strain bbqs395 ./P.bonniea_bbqs395.nanopore.fasta

`.faa` = Protein FASTA file of the translated sequences
`.ffn` = Nucleotide FASTA file of all the prediction transcripts
`.fna` = Nucleotide FASTA file of the input contig sequences.
`.gff` = Sequences and annotations
`.txt` = Statistics relating to the annotated features found.
`.tsv` = Seperated files of all features

**Q2**
Using `.txt` found 3430 CDS
using `.txt` there are 56 trna
using `.faa file` found 53 ribosomal proteins
1464 hypothetical proteins
can also use `grep "hypothetical protein"`
`PROKKAfilename | wc -l` and `grep "ribosomal protein" PROKKAfilename | wc -l`

**Q3**
`.tsv` is the most useful for finding genomic locations. It summarizes all the parts of the gene in which it is located and has the length.

**Q4**
My results were decently but not entirely accurate. This impacts my confidence positively although I am hesitant about the quality of the new draft genome.