---
# System prepended metadata

title: bi278 fall2022 lab practical

---

# bi278 fall2022 lab practical
## Olivia Schirle
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 oeschi23@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 .
cp /courses/bi278/Course_Materials/new_practical/*.fna . 
```

4. Find out which organisms the two genome files belong to.
```
grep ">" GCF_003019965.1_ASM301996v1_genomic.fna 
grep ">" GCF_020419785.1_ASM2041978v1_genomic.fna 
```
The genome files belong to *Burkholderia multivorans* and *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 both of the genomes are finished because the files contain the complete sequence or whole genome shotgun sequence. Also given that the organisms are found in the lungs of cystic fibrosis patients, I would expect that there would have been an effort to finish the genomes.

6. Find the genome size and GC% for the genome files.
```
grep -v ">" GCF_003019965.1_ASM301996v1_genomic.fna | tr -d -c ATGCatgc | wc -c
grep -v ">" GCF_003019965.1_ASM301996v1_genomic.fna | tr -d -c GCgc | wc -c
awk 'BEGIN {print (4251619/6322859)}'
grep -v ">" GCF_020419785.1_ASM2041978v1_genomic.fna | tr -d -c ATGCatgc | wc -c
grep -v ">" GCF_020419785.1_ASM2041978v1_genomic.fna | tr -d -c GCgc | wc -c
awk 'BEGIN {print (5487852/8195038)}'
```
The size of the *Burkholderia multivorans* genome is 6322859 bases. It has a GC% of 67.242%. The size of the *Burkholderia cepacia* genome is 8195038 bases. It has a GC% of 66.9655%.

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
fastq-dump --split-3 --skip-technical --readids --read-filter pass --dumpbase --clip -v --fasta default --outdir ~/practical SRR8885150
```

8. SRA reads have already been downloaded for you. How many reads are included in each `*SRR*.fasta` file?
```
grep ">" bmulti_SRR8885150.fasta | wc -l
grep ">" bceno_SRR2558789.fasta | wc -l
```
1636959 reads are included in the `bmulti_SRR8885150.fasta` file and 2608479 reads are included in the `bceno_SRR2558789.fasta` file.

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 bmulti.m29.count bmulti_SRR8885150.fasta
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 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 multivorans* | 6322859 | 6357976 |
| *Burkholderia cepacia* | 8195038 | 9662230 |

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



