---
# System prepended metadata

title: SHOT GUN

---

# SHOT GUN 

## Quality Check 

Program: FastQC (dowloand)

![](https://i.imgur.com/Xsntxva.png)
![](https://i.imgur.com/o7rK05u.png)
![](https://i.imgur.com/prWJjeE.png)


## Quality filter 

Program: SolexaQC (dowloand)

remove sequecie with low quality 

- [ ] do not do that when the quality check is ok 


`~/SolexaQA++_v3.1.7.1/MacOs_10.7+/SolexaQA++ dynamictrim A_R1_001.fastq.gz A_R1_001.fastq.gz --illumina -d solexa/ -h 3`

h : choose the parameter quality in graphic 

ex. for h = 3 

![](https://i.imgur.com/H6VQlZP.png)

mean = 98 , median = 116

ex. for h = 28 

![](https://i.imgur.com/zoNtOYg.png)

mean = 0 , median = 0 


![](https://i.imgur.com/5xv6sjj.png)

For L1:
mean = 98.8 , median = 116

For L2:
mean = 79.9 , median = 77

![](https://i.imgur.com/0Ck6hXo.png)

mean = 0 , median = 0


Before running prinseq, we need to create a folder to store the output files that are going to be create. This is derepl. Also, in the comand:
perl ~/prinseq-lite-0.20.4/prinseq-lite.pl -fastq L_1.fq -fastq2 L_2.fq -derep 1 -log derepl/"$x".log -out_good derepl/A, "$x" and A have to be replace by the name we want to save the file.
Without these changes we are going to get this error:
![](https://i.imgur.com/44EuFlT.png)

The results after running prinseq:
![](https://i.imgur.com/ge5p4Ae.png)


Checking quality again:
![](https://i.imgur.com/TQS3nWg.png)

If we see this error running SPAdes:
![](https://i.imgur.com/WIBCYbk.png)
the problem is the memory. We need to find out the suitable memory for us or work in another pc.

Checking the quality of assembly file with QUAST. In the code, we need to specify the contigs.fasta and scaffolds.fasta. The code here is to work with lot of files.

`/Users/Ilario/quast/quast.py contig/L.fasta contig/X.fasta```

![](https://i.imgur.com/Uj53L0d.png)


Correct file after QUAST analysis:
![](https://i.imgur.com/3QcXPAj.png)

For creating a command use nano and write down the code. To save it we need to Write Out the code (Ctrl+O) and put a name with the extension. We are going to use this code with perl so we need the pl extension.
If we have created the file without the extension, we open again nano and this time Read Out (Ctrl+R). Look for our file (looking for the name) and saving again as already explained.












