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# System prepended metadata

title: 9/13Lab1_Notes

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# 9/13Lab1_Notes
used `ssh bi278` to log into Unix
`ls` used as list command. Shows everything within the file you're in. `pwd` shows where you are
colbyhome command did not function
Entered lab_01a directory and copied course material into it
`cp /courses/bi278/Course_Materials/lab_01a/* ./lab_01a`
entered into lab_01a directory by typing `cd Lab_01a`
`mkdir` to rename as Trial 1
Used `rmdir Trial 1` to delete directory name
```Spelling is IMPORTANT. a single extra letter or incorrect punctuation will result in wrong command or no command```
created directory named achybrid using mkdir. Moved achybrid_reconciled_playback_predicted_final_2015.txt into the directory using `mv achybrid_reconciled_playback_predicted_final_2015.txt achybrid`
Organized further all files containing "songplot" into file "songplots", "raw_preference" into file "raw_preference", and any containing "achybrid" into "achybrid"

NOTE* exit directory using `cd ~`
Exercise 2
Organism	    Strain	   Contig count
P. agricolaris	baqs159	     2
P. bonniea	    bbqs859	     2
P. bonniea	    bbqs395	     2
P. bonniea		bbqs433.     2
P. fungorum		BAA463       4
P. hayleyella	bhqs155	     2
P. hayleyella	bhqs171.     35
P. hayleyella	bhqs21.      35
P. hayleyella	bhqs22       45
P. hayleyella	bhqs23       36
P. hayleyella	bhqs530.     2
P. hayleyella	bhqs69       2
P. hayleyella	BhQS11.      2
P. sprentiae	WSM5005      5	
P. terrae		DSM17804     4
P. xenovorans	LB400.       3	
THIS TOOK FOREVER
ex. `grep ">" /courses/bi278/Course_Materials/lab_01b/GCF_009455685.1_ASM945568v1_genomic.fna*`
grep ">" PATH/test.fa showed 1 contig
-v ">" PATH/test.fa counts all without header, "test"
 -v ">" PATH/test.fa | tr -d -c GCgc isolated just the G and Cs within the group
 -v ">" PATH/test.fa | tr -d -c GCgc | wc -c  showed a count of G and C
 `grep -v ">" /courses/bi278/Course_Materials/lab_01b/test.fa | tr -d -c GCATatgc | wc -c` showed total number of bases
 Used bottom three codes in nano to successfully save a file in nano
 It's almost 4 and I am not up to calculate the GC
 I tried please give me credit used whole lab period
 
 
 bceno_SRR2558789.fasta 
bmulti_SRR8885150.fasta 
GCF_003019965.1_ASM301996v1_genomic.fna 
GCF_020419785.1_ASM2041978v1_genomic.fna