RADcamp NYC

Columbia University, 2019

Introduction to RAD and the terminal


ipyrad command-line summary

1. create a params file


  $ ipyrad -n somename
                    

2. edit the params file (using a text editor)

  $ nano params-somename.txt  ## (edit, save, exit: ..., ctrl-o, ctrl-x)
                    

3. run ipyrad steps 1-7

  $ ipyrad -p params-somename.txt -s 1234567
                    

Connecting to google cloud instance


Enter given IP address into browser. No https// at beginning.

PATHs of interest on google cloud


  # home: the default location when you login
  /home/isaac_overcast/

  # 3RAD DATA directory (subdirectory for each dataset)
  /media/RADCamp/

  # Example files within a subdirectory
  ls /media/RADCamp/Meek
                    
    
  Meek_barcodes.txt
  raws/
                    

The (internal) barcodes file

Contains three items on each line, a name, the R1 barcode, and the read2 barcode.


  # show all contents of the barcode file
  cat /media/RADCamp/Meek/Meek_barcodes.txt
                    
    
Pedicularis_430 CCGAAT      ACGCAT
Pedicularis_442 TTAGGCA     ACGCAT
Pedicularis_431 AACTCGTC        ACGCAT
Pedicularis_13  GGTCTACGT       ACGCAT
Pedicularis_457 GATACC      ACGCAT
Pedicularis_455 AGCGTTG     ACGCAT
Pedicularis_429 CTGCAACT        ACGCAT
Pedicularis_25.1        TCATGGTCA       ACGCAT
Pedicularis_25.2        CCGAAT  GTATGCA
Pedicularis_39  TTAGGCA GTATGCA
Pedicularis_216 AACTCGTC        GTATGCA
Pedicularis_200 GGTCTACGT       GTATGCA
Pedicularis_31  GATACC  GTATGCA
Pedicularis_25.3        AGCGTTG GTATGCA
Pedicularis_421 CTGCAACT        GTATGCA
Pedicularis_38  TCATGGTCA       GTATGCA
                    

The raw un-demultiplexed data files

Paired data comes in two fastq files, one with _R1_ in the name and the other _R2_


  # Example files within a subdirectory
  ls /media/RADCamp/Meek/raws
                        
    
  19174FL-01-01-21_S21_R1_001.fastq.gz
  19174FL-01-01-21_S21_R2_001.fastq.gz  
                        

Which cutters did I use again?

You can always do a google search on your enzyme to find the overhang sequence that you expect to have attached to your reads. But I always recommend looking for it in your data directly. It will occur near the beginning of R1 or R2 and a common sequence after the barcode.

    
  # use tab-completion to enter this long file path
  less /media/RADCamp/Meek/raws/19174FL-01-01-21_S21_R1_001.fastq.gz                      
                    

Which cutters did I use again?

Once inside of less, press the / key once and you will see a prompt open in the lower left. Type ATCGG then Enter. This will highlight matches. Press q at any time to exit.

Look for cutters in R1 and R2 of a different file.

Every data set used one set or the other: (EcoRI, NheI) or (BamHI, ClaI). As we did in the last slide, search for the sequences below in one or more data files using less.

In R1 files try one of the following:
BamHI: ATCGG (G/A)
EcoRI: GCTAG (A/C)

In R1 files try one of the following:
ClaI: CGATCC
NheI: TAATTC

Declone PCR duplicates w/ i5 tags

3RAD can incorporate a unique molecular identifiers (UMI) into the i5 index.


Standard data without i7 and i5 tags

@NB551405:60:H7T2GAFXY:1:11101:20590:1124 1:N:0:
AACTCGTCATCGGCATAAGCTAGACCATCTAAAGAACTTTTAAGACTAAAGCGGCATAAGCTAGACC...
+
AABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB...


The data with i7 and i5 tags attached to reads

@NB551405:60:H7T2GAFXY:1:11101:20590:1124 1:N:0: CTCGTCAT+GATTGCCA
AACTCGTCATCGGCATAAGCTAGACCATCTAAAGAACTTTTAAGACTAAAGCGGCATAAGCTAATCT...
+
AABBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB...

Getting started on real data

Let's all put our assemblies in a folders with the same name to make things simple.

  # move to your home directory
  $ cd

  # from here, make a directory in which to store all our work
  $ mkdir empirical

  # move into empirical 
  $ cd empirical/

  # create a new params file and name it with your data set's name
  $ ipyrad -n Meek
                    

My DENOVO paired 3RAD params

Ask for help if you are working on a different data set than one already on the cloud. We can help you to set up your params. Other cutter pair is GCTAG, TAATTC.



  /media/RADCamp/Meek/raws/*_R*.fastq.gz    ## [2] [raw_fastq_path]: ...
  /media/RADCamp/Meek/Meek_barcodes.txt     ## [3] [barcodes_path]: ...

  pair3rad                                  ## [7] [datatype]: ...
  ATCGG, CGATCC                             ## [8] [restriction_overhang]: ...

  1                                         ## [15] [max_barcode_mismatch]: ...
  2                                         ## [16] [filter_adapters]: ...
                               
                    

My REFERENCE paired 3RAD params

If your study organism has a closely related (~20Ma or less) published high quality genome available then download the FASTA file to your empirical/ directory.



  /media/RADCamp/Meek/raws/*_R*.fastq.gz    ## [2] [raw_fastq_path]: ...
  /media/RADCamp/Meek/Meek_barcodes.txt     ## [3] [barcodes_path]: ...

  reference                                 ## [5] [assembly_method]: ...
  reference_file.fa                         ## [6] [reference_sequence]...
  pair3rad                                  ## [7] [datatype]: ...
  ATCGG, CGATCC                             ## [8] [restriction_overhang]: ...

  1                                         ## [15] [max_barcode_mismatch]: ...
  2                                         ## [16] [filter_adapters]: ...
                               
                    

START YOUR ASSEMBLY!


Set it to run all seven steps and then you're done for now. Let's go get pizza. We can check in on it as it runs later. It will probably finish in 1-3 hours.


  # start running all steps for your assembly
  $ ipyrad -p params-Meek.txt -s 1234567 
                    

Checking on it while it runs


You can disconnect and reconnect as much as you want, this is running in a terminal on the cloud server. The easiest way to check the stats of your run while it is running is to look at the stats files from the file browser in the jupyter server interface.