# LAB2
Using Salmonella enterica
mv /personal/dkalde22/lab\ 2\ Genomics/GCF_000054005.1_ASM5400v1_genomic.fna ~ to access file in terminal
ls
Stuck idk what shell is
Couldn't find my basecounting command
SO, used ls /home/students/d/dkalde22 to see if I had it
Then used mv /home/students/d/dkalde22/lab_01a to move it into my home
used 'sh lab_01a/CountingBases.sh fasta_pasta GCF_000054005.1_ASM5400v1_genomic.fna ' but it didn't work and I suspect my fastapasta is non-functional
Selected SRR12379546
Used command 'fastq-dump -X 3 -Z SRR12379546' to access
'fastq-dump -–split-3 --skip-technical --readids --read-filter pass --
dumpbase --clip -v --fasta default
--outdir ~/lab_02 SR12379546'
MAKE SURE YOU KNOW IF ITS FASTA OR FASTQ, Dexter
Organism Estimated Size
P. Sprentiae

| Organism | Genome Size | Estimated Size |
| -------- | ----------- | -------------- |
| P. Sprentiae |7829542 | |
| S. Enterica | Text | Text |

Moved SRR3927471_pass_1.fasta and SRR12379546 into files "P.Sprentiae" and "Salmon", respectively using
'mv lab_02/SRR3927471_pass_2.fasta P.Sprentiae'
Attempted to 'jellyfish count -t 2 -C -s 1G -m 29 -o name.m29.count input_file' didn't have enough space so we are looking at Class generated
'ls /courses/bi278/Course_Materials/lab_02/'
copied pfung.m29.histo into Rstudio using 'cp /courses/bi278/Course_Materials/lab_02/pfung.m29.histo home2'
Renamed with mv home2 pfung.m29.histo
NOW IN R STUDIO
pfung.m29.histo <- read.table("pfung.m29.histo", h=F, sep="") to access table
> plot (pfung.m29.histo, type="1") to plot data from table
> plot(pfung.m29.histo[5:250,], type="l") yielded visible results
> 
159 was found to be highest density with 132689

nrow(name)
head(name)
head(name[,1]) #square brackets are used to limit [row, column]
head(name[,2])
head(name[5:nrow(name),])
head(name[5:nrow(name),1]*name[5:nrow(name),2])
sum(name[5:nrow(name),1]*name[5:nrow(name),2])
sum(name[5:nrow(name),1]*name[5:nrow(name),2])/159
yielded 8896343
It's 4:16 I am so tired and must nap.