---
# System prepended metadata

title: Alissa Doucet- Amsonia tharpii Project
tags: [RADSeq]

---

---
title: "Alissa Doucet- Amsonia tharpii Project"
breaks: false
tags: RADSeq
---

# Buxbaumia 

## Login

### Away from CBG: 
Login to Forticlient- VPN to access Fabronmia and Buxbaumia (See email)
### At CBG: 
Need to be at CBG to download files onto my computer: 
Open Windows Powershell
Login to fabromia (Jeremie's login info), then buxbaumia (Dylan's login info)

### Get to where data is:
**Change directory three times:**

cd .. 

    cd ..

        cd ..

**List what's in folder:** 

ls

**To go to specific folder:** 

(cd folder/)

    cd data

        cd Alissa (my data folder)



Stacks
===
### Overview
**1. Radtags:** Clean-up and demultiplex (do this with each sublibrary idividually)
**2. Denovomap:** Combine all sublibraries into one folder; assemble loci, call SNPs, based on parameter choices; output vcf files and basic pop stats; can refine parameters with python script
**3. Clean and use this output for analyses**


 
 

### 1. Process Radtags
1. nano barsub1.txt
2. save - control x
3. Remove files
    4. rm barcode.txt
5. Remove folder
    6. rm -rf test3
7. Make folder
    8. mkdir (make directory)
9. Create new folder
    10. mkdir sublib1
11. Note:
    12. Folders (blue)
    13. gunzipped files (red)
    14.text files, scripts (white)
15.nano process_radtag (copy code)

### Run Script
sh process_radtags.sh
enter

### Check to see if it's working
cat process_radtags1.out

cp = copy/paste

cp process_radtags.sh (duplicate file under new name)

cp process_radtags.sh (file name I want to copy)

process_radtags2.sh (new file name)

top = see who is using Buxbaumia

can process 2-3 radtags at a time

q = get out

### How to know whena job is done
If run at noon, check around 4-5pm. If done, will shoe in output file when its odne running; will summarize info from run at the bottom

### Notes
When copy/pasting barcodes into file, must use up arrow rather than scroll to see all 48 samples

01/26/2023
Processed Radtags for sublibaries #1-#10

### DeNovo Assembly 
denovo_map.[d]1-h (denovo help file)

Navigate to my folder

cd sublib1

[process_radtags.log] (can check reads here)

1. Remove files ending in rem.1.fq.gz & rem.2.gq.gz

**zless** file name (view in zip file) or raw sequence data
**less** 
