---
# System prepended metadata

title: bi278 fall2022 lab practical

---

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`.

ssh jereil26@bi278.colby.edu

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 GCF_020419785.1_ASM2041978v1_genomic.fna  ~/practical

cp GCF_003019965.1_ASM301996v1_genomic.fna ~/practical

cp bmulti_SRR8885150.fasta ~/practical

cp bceno_SRR2558789.fasta ~/practical
```

4. Find out which organisms the two genome files belong to.
```
cat GCF_003019965.1_ASM301996v1_genomic.fna - Burkholderia multivorans

cat 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 that these genomes are most likely finished. This is because these two organisms are bacteria (smaller and easily sequencable genome), and that there are no gaps within their genome sequence as seen by the cat command. This all points to a finished genome.

6. Find the genome size and GC% for the genome files.
```
grep -v ">" ./GCF_020419785.1_ASM2041978v1_genomic.fna | tr -d -c GCgc | wc -c
Burkholderia cepacia- 5487852 (GC Only)

practical]$ grep -v ">" ./GCF_020419785.1_ASM2041978v1_genomic.fna | tr -d -c GCATgcat | wc -c
Burkholderia cepacia- 8195038 (Genome size)

Burkholderia cepacia- GC%= 66.965%

grep -v ">" ./GCF_003019965.1_ASM301996v1_genomic.fna | tr -d -c GCgc | wc -c
Burkholderia multivorans- 4251619 (GC Only)

grep -v ">" ./GCF_003019965.1_ASM301996v1_genomic.fna | tr -d -c GCATgcat | wc -c
Burkholderia multivorans- 6322859 (Genome size)

Burkholderia multivorans- GC%= 67.242%


```

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 ~/practical SRR2558789
```
the "practical" is the name of the folder you want to put the download into. This can change depending on where you want the download to go. I chose the folder "practical", because that is where I would put it if I were to do it right now.

8. SRA reads have already been downloaded for you. How many reads are included in each `*SRR*.fasta` file?
```
cat bceno_SRR2558789.fasta
cat bmulti_SRR8885150.fasta

bceno_SRR2558789.fasta- 2608479 reads
bmulti_SRR8885150.fasta- 1636959 reads
```

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.29.count bceno_SRR2558789.fasta

jellyfish count -t 2 -C -s 1G -m 29 -o bmulti.29.count bmulti_SRR8885150.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 bmulti.m29.histo /courses/bi278/Course_Materials/new_practical/bmulti.m29.count

jellyfish histo -o bceno.m29.histo /courses/bi278/Course_Materials/new_practical/bceno.m29.count
```

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 cepacia     | 8195038     | 8655747     |
| Burkholderia multivorans | 6322859     | 6357976     |


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



