---
# System prepended metadata

title: bi278 fall2022 lab practical

---

# bi278 fall2022 lab practical
First, make a copy of the markdown version of this page. Then fill in the commands to execute each step with a: 
```
code block
```
Answer any  questions and fill any tables. 


*Reminder that `ls` and autocomplete will be your best friends.*

0. SSH onto `bi278`.

1. Make a new directory called 'practical'.
```
'mkdir practical'
```

2. Now go into this directory.
```
cd practical
```

3. Copy only the fasta files (`*.fasta` and `*.fna`) from `/courses/bi278/Course_Materials/practical` to your current location.
```
'cp /courses/bi278/Course_Materials/new_practical/*.fasta practical'
'cp /courses/bi278/Course_Materials/new_practical/*.fna practical'
```

4. Find out which organisms the two genome files belong to.
```
'grep ">" /practical GCF_003019965.1_ASM301996v1_genomic.fna'
--> Burkholderia multivorans
'grep ">" /practical GCF_020419785.1_ASM2041978v1_genomic.fna'
--> Burkholderia cepacia

5. These two organisms are close relatives, often found in the lungs of cystic fibrosis patients. Given this fact and based on what is contained in these genome files, what would you determine is the status of each genome? Choose between the options: draft or finished. Explain why. 
I believe the Burkholderia multivorans is a finished genome because it only has 3 contigs and says "complete sequence". The individual contigs/nodes are far longer than the other one, too. 
The Burkholderia cepacia has many many contigs with far shorter lengths so I believe this one is a draft. 

6. Find the genome size and GC% for the genome files.
```
'grep -v ">" /practical GCF_020419785.1_ASM2041978v1_genomic.fna | tr -d -c GCgcATat | wc -c'
--> 8809768 = total
'grep -v ">" /practical GCF_020419785.1_ASM2041978v1_genomic.fna | tr -d -c GCgc | wc -c'
--> 5897672
GC% = 66.9%
grep -v ">" /practical GCF_003019965.1_ASM301996v1_genomic.fna | tr -d -c GCgcATat | wc -c
--> 6797081

grep -v ">" /practical GCF_003019965.1_ASM301996v1_genomic.fna | tr -d -c GCgcATat | wc -c
4567767
GC% = 67.2%
7. What is the appropriate command to download the raw sequencing reads from this sample? **(but don't run it)** https://www.ncbi.nlm.nih.gov/sra/SRX1304848[accn]
```
‘fastq-dump -–split-3 --skip-technical --readids --read-filter pass –
dumpbase --clip -v --fasta default
–outdir ~/SRR2558789’
```

8. SRA reads have already been downloaded for you. How many reads are included in each `*SRR*.fasta` file?
```
Tried grep ">" /practical bceno_SRR2558789.fasta but it was too many reads to count and i don't know how to just get a number
```

9. `jellyfish count` has already been run for you on both SRA files and left in the remote "practical" directory above. Recreate at least one of the commands that was used to do this task **(but don't run it)**. Make sure the input and output file names correspond to the files in the remote directory.
```
jellyfish count -t 2 -C -s 1G -m 29 -o bceno.m29.count bceno_SRR2558789.fasta’
```

10. Run `jellyfish histo` on both of the `*.count` files still in the remote directory, without copying them to your current directory.
```
'jellyfish histo -o bceno.m29.histo /courses/bi278/Course_Materials/new_practical/bceno.m29.count'
```
Kinda blew up the computer but i think it worked.

11. Import the resulting `*.histo` files into R and estimate each genome size based on their kmer curves. No need to report R code back but fill in the table.


| Organism | Genome size (basepair count from step 6) | Genome size (kmer estimate) |
| -------- | -------- | -------- |
| Burkholderia multivorans    |   6797081   | 6357976     |
| Burkholderia cepacia    | 8809768    | 9662230    |


12. Exit out of your SSH connection.
```

```



