---
# System prepended metadata

title: BI178 Practical

---

# BI178 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.
```
cd
cp /courses/bi278/Course_Materials/new_practical/*.fasta practical
```

4. Find out which organisms the two genome files belong to.
```
bceno_SRR2558789.fasta #Burkholderia cenocepacia
bmulti_SRR8885150.fasta #Burkholderia multivorans
```

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. 

Using the .fna files (GCF), I looked at the content of the files. The B. Multi file had 2 completed chromosomes and one completed plasmid, while the B. Cepacia file had many shotgun sequences. This suggests that the B. Multi is likely a finished genome (no fragments, fully assembled), while the B. Ceno genome is likely a draft because of the number of shotgun sequences. 

6. Find the genome size and GC% for the genome files.
```
cd
cd lab_02
nano
#I copied the shell script for GC%_genomesize. sh into practical
    grep -v ">" /home2/cgsnow25/practical/$1 |tr -d -c ATGCatgc | wc -c 
    grep -v ">" /home2/cgsnow25/practical/$1 |tr -d -c GCgc | wc -c 
sh GC%_genomesize.sh bceno_SRR2558789.fasta
sh GC%_genomesize.sh bmulti_SRR8885150.fasta
```
B. Ceno genome size was 506435753, GC% was 64.91% (content 161999073)
B. Multi genome size 239967045, GC% was 67.50% (content 161999073)

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
#run again, replacing SRR2558789 for SRR8885150
```

8. SRA reads have already been downloaded for you. How many reads are included in each `*SRR*.fasta` file?
```
tail -20 bceno_SRR2558789.fasta
tail -20 
```
B. Ceno: 2608479
B. Multi: 1636959

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 20 -o bceno.m20.count bceno_SRR2558789.fasta
jellyfish count -t 2 -C -s 1G -m 20 -o bmulti.m20.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 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) |
| -------- | -------- | -------- |
| B. cenocepacia     | 506435753     | 9662230     |
| B. multivorans     | 239967045     | 6357976     |


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



