Notebook

In [1]:

%%bash
date

Thu Apr 28 10:05:32 PDT 2016

In [2]:

%%bash
system_profiler SPSoftwareDataType

Software:

    System Software Overview:

      System Version: OS X 10.9.5 (13F34)
      Kernel Version: Darwin 13.4.0
      Boot Volume: Hummingbird
      Boot Mode: Normal
      Computer Name: hummingbird
      User Name: Sam (Sam)
      Secure Virtual Memory: Enabled
      Time since boot: 10 days 11 minutes

In [3]:

%%bash
#Uses grep to exclude lines that display serial number and hardware UUID
system_profiler SPHardwareDataType | grep -v [SH][ea]


      Model Name: Xserve
      Model Identifier: Xserve3,1
      Processor Name: Quad-Core Intel Xeon
      Processor Speed: 2.26 GHz
      Number of Processors: 2
      Total Number of Cores: 8
      L2 Cache (per Core): 256 KB
      L3 Cache (per Processor): 8 MB
      Memory: 24 GB
      Processor Interconnect Speed: 5.86 GT/s
      Boot ROM Version: XS31.0081.B06
      SMC Version (system): 1.43f4
      LOM Revision: 1.1.8

Move to directory with GBS FASTQ files¶

In [20]:

cd /Volumes/toaster/sam/scratch/20160428_Oly_GBS_stacks/

/Volumes/toaster/sam/scratch/20160428_Oly_GBS_stacks

List all FASTQ files for use in subsequent STACKS command¶

In [22]:

%%bash
echo *_1.fq.gz

1HL_10A_1.fq.gz 1HL_11A_1.fq.gz 1HL_12A_1.fq.gz 1HL_13A_1.fq.gz 1HL_14A_1.fq.gz 1HL_15A_1.fq.gz 1HL_16A_1.fq.gz 1HL_17A_1.fq.gz 1HL_19A_1.fq.gz 1HL_1A_1.fq.gz 1HL_20A_1.fq.gz 1HL_21A_1.fq.gz 1HL_22A_1.fq.gz 1HL_23A_1.fq.gz 1HL_24A_1.fq.gz 1HL_25A_1.fq.gz 1HL_26A_1.fq.gz 1HL_27A_1.fq.gz 1HL_28A_1.fq.gz 1HL_29A_1.fq.gz 1HL_2A_1.fq.gz 1HL_31A_1.fq.gz 1HL_33A_1.fq.gz 1HL_34A_1.fq.gz 1HL_35A_1.fq.gz 1HL_3A_1.fq.gz 1HL_4A_1.fq.gz 1HL_5A_1.fq.gz 1HL_6A_1.fq.gz 1HL_7A_1.fq.gz 1HL_8A_1.fq.gz 1HL_9A_1.fq.gz 1NF_10A_1.fq.gz 1NF_11A_1.fq.gz 1NF_12A_1.fq.gz 1NF_13A_1.fq.gz 1NF_14A_1.fq.gz 1NF_15A_1.fq.gz 1NF_16A_1.fq.gz 1NF_17A_1.fq.gz 1NF_18A_1.fq.gz 1NF_19A_1.fq.gz 1NF_1A_1.fq.gz 1NF_20A_1.fq.gz 1NF_21A_1.fq.gz 1NF_22A_1.fq.gz 1NF_23A_1.fq.gz 1NF_24A_1.fq.gz 1NF_25A_1.fq.gz 1NF_26A_1.fq.gz 1NF_27A_1.fq.gz 1NF_28A_1.fq.gz 1NF_29A_1.fq.gz 1NF_2A_1.fq.gz 1NF_30A_1.fq.gz 1NF_31A_1.fq.gz 1NF_32A_1.fq.gz 1NF_33A_1.fq.gz 1NF_4A_1.fq.gz 1NF_5A_1.fq.gz 1NF_6A_1.fq.gz 1NF_7A_1.fq.gz 1NF_8A_1.fq.gz 1NF_9A_1.fq.gz 1SN_10A_1.fq.gz 1SN_11A_1.fq.gz 1SN_12A_1.fq.gz 1SN_13A_1.fq.gz 1SN_14A_1.fq.gz 1SN_15A_1.fq.gz 1SN_16A_1.fq.gz 1SN_17A_1.fq.gz 1SN_18A_1.fq.gz 1SN_19A_1.fq.gz 1SN_1A_1.fq.gz 1SN_20A_1.fq.gz 1SN_21A_1.fq.gz 1SN_22A_1.fq.gz 1SN_23A_1.fq.gz 1SN_24A_1.fq.gz 1SN_25A_1.fq.gz 1SN_26A_1.fq.gz 1SN_27A_1.fq.gz 1SN_28A_1.fq.gz 1SN_29A_1.fq.gz 1SN_2A_1.fq.gz 1SN_30A_1.fq.gz 1SN_31A_1.fq.gz 1SN_32A_1.fq.gz 1SN_3A_1.fq.gz 1SN_4A_1.fq.gz 1SN_5A_1.fq.gz 1SN_6A_1.fq.gz 1SN_7A_1.fq.gz 1SN_8A_1.fq.gz 1SN_9A_1.fq.gz UnKnow_1.fq.gz

In [23]:

%%bash
echo *_2.fq.gz

1HL_10A_2.fq.gz 1HL_11A_2.fq.gz 1HL_12A_2.fq.gz 1HL_13A_2.fq.gz 1HL_14A_2.fq.gz 1HL_15A_2.fq.gz 1HL_16A_2.fq.gz 1HL_17A_2.fq.gz 1HL_19A_2.fq.gz 1HL_1A_2.fq.gz 1HL_20A_2.fq.gz 1HL_21A_2.fq.gz 1HL_22A_2.fq.gz 1HL_23A_2.fq.gz 1HL_24A_2.fq.gz 1HL_25A_2.fq.gz 1HL_26A_2.fq.gz 1HL_27A_2.fq.gz 1HL_28A_2.fq.gz 1HL_29A_2.fq.gz 1HL_2A_2.fq.gz 1HL_31A_2.fq.gz 1HL_33A_2.fq.gz 1HL_34A_2.fq.gz 1HL_35A_2.fq.gz 1HL_3A_2.fq.gz 1HL_4A_2.fq.gz 1HL_5A_2.fq.gz 1HL_6A_2.fq.gz 1HL_7A_2.fq.gz 1HL_8A_2.fq.gz 1HL_9A_2.fq.gz 1NF_10A_2.fq.gz 1NF_11A_2.fq.gz 1NF_12A_2.fq.gz 1NF_13A_2.fq.gz 1NF_14A_2.fq.gz 1NF_15A_2.fq.gz 1NF_16A_2.fq.gz 1NF_17A_2.fq.gz 1NF_18A_2.fq.gz 1NF_19A_2.fq.gz 1NF_1A_2.fq.gz 1NF_20A_2.fq.gz 1NF_21A_2.fq.gz 1NF_22A_2.fq.gz 1NF_23A_2.fq.gz 1NF_24A_2.fq.gz 1NF_25A_2.fq.gz 1NF_26A_2.fq.gz 1NF_27A_2.fq.gz 1NF_28A_2.fq.gz 1NF_29A_2.fq.gz 1NF_2A_2.fq.gz 1NF_30A_2.fq.gz 1NF_31A_2.fq.gz 1NF_32A_2.fq.gz 1NF_33A_2.fq.gz 1NF_4A_2.fq.gz 1NF_5A_2.fq.gz 1NF_6A_2.fq.gz 1NF_7A_2.fq.gz 1NF_8A_2.fq.gz 1NF_9A_2.fq.gz 1SN_10A_2.fq.gz 1SN_11A_2.fq.gz 1SN_12A_2.fq.gz 1SN_13A_2.fq.gz 1SN_14A_2.fq.gz 1SN_15A_2.fq.gz 1SN_16A_2.fq.gz 1SN_17A_2.fq.gz 1SN_18A_2.fq.gz 1SN_19A_2.fq.gz 1SN_1A_2.fq.gz 1SN_20A_2.fq.gz 1SN_21A_2.fq.gz 1SN_22A_2.fq.gz 1SN_23A_2.fq.gz 1SN_24A_2.fq.gz 1SN_25A_2.fq.gz 1SN_26A_2.fq.gz 1SN_27A_2.fq.gz 1SN_28A_2.fq.gz 1SN_29A_2.fq.gz 1SN_2A_2.fq.gz 1SN_30A_2.fq.gz 1SN_31A_2.fq.gz 1SN_32A_2.fq.gz 1SN_3A_2.fq.gz 1SN_4A_2.fq.gz 1SN_5A_2.fq.gz 1SN_6A_2.fq.gz 1SN_7A_2.fq.gz 1SN_8A_2.fq.gz 1SN_9A_2.fq.gz UnKnow_2.fq.gz

Run QC on files with `process_radtags` component¶

Cell below creates two lists (one list for each individual pair of FASTQs), loops through each as an array and assigns the corresponding FASTQ pairs to the variables "i" and "j". The values in "i" and "j" are used in the `process_radtags` command for matching the paired FASTQ files.¶

In [24]:

%%bash
seq1=( 1HL_10A_1.fq.gz 1HL_11A_1.fq.gz 1HL_12A_1.fq.gz 1HL_13A_1.fq.gz 1HL_14A_1.fq.gz 1HL_15A_1.fq.gz 1HL_16A_1.fq.gz 1HL_17A_1.fq.gz 1HL_19A_1.fq.gz 1HL_1A_1.fq.gz 1HL_20A_1.fq.gz 1HL_21A_1.fq.gz 1HL_22A_1.fq.gz 1HL_23A_1.fq.gz 1HL_24A_1.fq.gz 1HL_25A_1.fq.gz 1HL_26A_1.fq.gz 1HL_27A_1.fq.gz 1HL_28A_1.fq.gz 1HL_29A_1.fq.gz 1HL_2A_1.fq.gz 1HL_31A_1.fq.gz 1HL_33A_1.fq.gz 1HL_34A_1.fq.gz 1HL_35A_1.fq.gz 1HL_3A_1.fq.gz 1HL_4A_1.fq.gz 1HL_5A_1.fq.gz 1HL_6A_1.fq.gz 1HL_7A_1.fq.gz 1HL_8A_1.fq.gz 1HL_9A_1.fq.gz 1NF_10A_1.fq.gz 1NF_11A_1.fq.gz 1NF_12A_1.fq.gz 1NF_13A_1.fq.gz 1NF_14A_1.fq.gz 1NF_15A_1.fq.gz 1NF_16A_1.fq.gz 1NF_17A_1.fq.gz 1NF_18A_1.fq.gz 1NF_19A_1.fq.gz 1NF_1A_1.fq.gz 1NF_20A_1.fq.gz 1NF_21A_1.fq.gz 1NF_22A_1.fq.gz 1NF_23A_1.fq.gz 1NF_24A_1.fq.gz 1NF_25A_1.fq.gz 1NF_26A_1.fq.gz 1NF_27A_1.fq.gz 1NF_28A_1.fq.gz 1NF_29A_1.fq.gz 1NF_2A_1.fq.gz 1NF_30A_1.fq.gz 1NF_31A_1.fq.gz 1NF_32A_1.fq.gz 1NF_33A_1.fq.gz 1NF_4A_1.fq.gz 1NF_5A_1.fq.gz 1NF_6A_1.fq.gz 1NF_7A_1.fq.gz 1NF_8A_1.fq.gz 1NF_9A_1.fq.gz 1SN_10A_1.fq.gz 1SN_11A_1.fq.gz 1SN_12A_1.fq.gz 1SN_13A_1.fq.gz 1SN_14A_1.fq.gz 1SN_15A_1.fq.gz 1SN_16A_1.fq.gz 1SN_17A_1.fq.gz 1SN_18A_1.fq.gz 1SN_19A_1.fq.gz 1SN_1A_1.fq.gz 1SN_20A_1.fq.gz 1SN_21A_1.fq.gz 1SN_22A_1.fq.gz 1SN_23A_1.fq.gz 1SN_24A_1.fq.gz 1SN_25A_1.fq.gz 1SN_26A_1.fq.gz 1SN_27A_1.fq.gz 1SN_28A_1.fq.gz 1SN_29A_1.fq.gz 1SN_2A_1.fq.gz 1SN_30A_1.fq.gz 1SN_31A_1.fq.gz 1SN_32A_1.fq.gz 1SN_3A_1.fq.gz 1SN_4A_1.fq.gz 1SN_5A_1.fq.gz 1SN_6A_1.fq.gz 1SN_7A_1.fq.gz 1SN_8A_1.fq.gz 1SN_9A_1.fq.gz )
seq2=( 1HL_10A_2.fq.gz 1HL_11A_2.fq.gz 1HL_12A_2.fq.gz 1HL_13A_2.fq.gz 1HL_14A_2.fq.gz 1HL_15A_2.fq.gz 1HL_16A_2.fq.gz 1HL_17A_2.fq.gz 1HL_19A_2.fq.gz 1HL_1A_2.fq.gz 1HL_20A_2.fq.gz 1HL_21A_2.fq.gz 1HL_22A_2.fq.gz 1HL_23A_2.fq.gz 1HL_24A_2.fq.gz 1HL_25A_2.fq.gz 1HL_26A_2.fq.gz 1HL_27A_2.fq.gz 1HL_28A_2.fq.gz 1HL_29A_2.fq.gz 1HL_2A_2.fq.gz 1HL_31A_2.fq.gz 1HL_33A_2.fq.gz 1HL_34A_2.fq.gz 1HL_35A_2.fq.gz 1HL_3A_2.fq.gz 1HL_4A_2.fq.gz 1HL_5A_2.fq.gz 1HL_6A_2.fq.gz 1HL_7A_2.fq.gz 1HL_8A_2.fq.gz 1HL_9A_2.fq.gz 1NF_10A_2.fq.gz 1NF_11A_2.fq.gz 1NF_12A_2.fq.gz 1NF_13A_2.fq.gz 1NF_14A_2.fq.gz 1NF_15A_2.fq.gz 1NF_16A_2.fq.gz 1NF_17A_2.fq.gz 1NF_18A_2.fq.gz 1NF_19A_2.fq.gz 1NF_1A_2.fq.gz 1NF_20A_2.fq.gz 1NF_21A_2.fq.gz 1NF_22A_2.fq.gz 1NF_23A_2.fq.gz 1NF_24A_2.fq.gz 1NF_25A_2.fq.gz 1NF_26A_2.fq.gz 1NF_27A_2.fq.gz 1NF_28A_2.fq.gz 1NF_29A_2.fq.gz 1NF_2A_2.fq.gz 1NF_30A_2.fq.gz 1NF_31A_2.fq.gz 1NF_32A_2.fq.gz 1NF_33A_2.fq.gz 1NF_4A_2.fq.gz 1NF_5A_2.fq.gz 1NF_6A_2.fq.gz 1NF_7A_2.fq.gz 1NF_8A_2.fq.gz 1NF_9A_2.fq.gz 1SN_10A_2.fq.gz 1SN_11A_2.fq.gz 1SN_12A_2.fq.gz 1SN_13A_2.fq.gz 1SN_14A_2.fq.gz 1SN_15A_2.fq.gz 1SN_16A_2.fq.gz 1SN_17A_2.fq.gz 1SN_18A_2.fq.gz 1SN_19A_2.fq.gz 1SN_1A_2.fq.gz 1SN_20A_2.fq.gz 1SN_21A_2.fq.gz 1SN_22A_2.fq.gz 1SN_23A_2.fq.gz 1SN_24A_2.fq.gz 1SN_25A_2.fq.gz 1SN_26A_2.fq.gz 1SN_27A_2.fq.gz 1SN_28A_2.fq.gz 1SN_29A_2.fq.gz 1SN_2A_2.fq.gz 1SN_30A_2.fq.gz 1SN_31A_2.fq.gz 1SN_32A_2.fq.gz 1SN_3A_2.fq.gz 1SN_4A_2.fq.gz 1SN_5A_2.fq.gz 1SN_6A_2.fq.gz 1SN_7A_2.fq.gz 1SN_8A_2.fq.gz 1SN_9A_2.fq.gz )
time for pair in "${!seq1[@]}"; do
  i=${seq1[$pair]}
  j=${seq2[$pair]}
  /usr/local/bioinformatics/stacks-1.37/process_radtags \
  -1 $i \
  -2 $j \
  -o /Volumes/toaster/sam/scratch/20160428_Oly_GBS_stacks/ \
  -e apeKI \
  -c \
  -q \
  -i gzfastq \
  >>radtags.stdout 2>>radtags.stderr
done

real	386m2.612s
user	381m30.306s
sys	2m20.472s

Concatenate `process_radtags` output files into single FASTQ file¶

Create four lists - each of the four output files generated per individual for use in subsequent concatenation command.¶

In [ ]:

In [25]:

%%bash
list1=( 1HL_10A_1.1.fq.gz 1HL_11A_1.1.fq.gz 1HL_12A_1.1.fq.gz 1HL_13A_1.1.fq.gz 1HL_14A_1.1.fq.gz 1HL_15A_1.1.fq.gz 1HL_16A_1.1.fq.gz 1HL_17A_1.1.fq.gz 1HL_19A_1.1.fq.gz 1HL_1A_1.1.fq.gz 1HL_20A_1.1.fq.gz 1HL_21A_1.1.fq.gz 1HL_22A_1.1.fq.gz 1HL_23A_1.1.fq.gz 1HL_24A_1.1.fq.gz 1HL_25A_1.1.fq.gz 1HL_26A_1.1.fq.gz 1HL_27A_1.1.fq.gz 1HL_28A_1.1.fq.gz 1HL_29A_1.1.fq.gz 1HL_2A_1.1.fq.gz 1HL_31A_1.1.fq.gz 1HL_33A_1.1.fq.gz 1HL_34A_1.1.fq.gz 1HL_35A_1.1.fq.gz 1HL_3A_1.1.fq.gz 1HL_4A_1.1.fq.gz 1HL_5A_1.1.fq.gz 1HL_6A_1.1.fq.gz 1HL_7A_1.1.fq.gz 1HL_8A_1.1.fq.gz 1HL_9A_1.1.fq.gz 1NF_10A_1.1.fq.gz 1NF_11A_1.1.fq.gz 1NF_12A_1.1.fq.gz 1NF_13A_1.1.fq.gz 1NF_14A_1.1.fq.gz 1NF_15A_1.1.fq.gz 1NF_16A_1.1.fq.gz 1NF_17A_1.1.fq.gz 1NF_18A_1.1.fq.gz 1NF_19A_1.1.fq.gz 1NF_1A_1.1.fq.gz 1NF_20A_1.1.fq.gz 1NF_21A_1.1.fq.gz 1NF_22A_1.1.fq.gz 1NF_23A_1.1.fq.gz 1NF_24A_1.1.fq.gz 1NF_25A_1.1.fq.gz 1NF_26A_1.1.fq.gz 1NF_27A_1.1.fq.gz 1NF_28A_1.1.fq.gz 1NF_29A_1.1.fq.gz 1NF_2A_1.1.fq.gz 1NF_30A_1.1.fq.gz 1NF_31A_1.1.fq.gz 1NF_32A_1.1.fq.gz 1NF_33A_1.1.fq.gz 1NF_4A_1.1.fq.gz 1NF_5A_1.1.fq.gz 1NF_6A_1.1.fq.gz 1NF_7A_1.1.fq.gz 1NF_8A_1.1.fq.gz 1NF_9A_1.1.fq.gz 1SN_10A_1.1.fq.gz 1SN_11A_1.1.fq.gz 1SN_12A_1.1.fq.gz 1SN_13A_1.1.fq.gz 1SN_14A_1.1.fq.gz 1SN_15A_1.1.fq.gz 1SN_16A_1.1.fq.gz 1SN_17A_1.1.fq.gz 1SN_18A_1.1.fq.gz 1SN_19A_1.1.fq.gz 1SN_1A_1.1.fq.gz 1SN_20A_1.1.fq.gz 1SN_21A_1.1.fq.gz 1SN_22A_1.1.fq.gz 1SN_23A_1.1.fq.gz 1SN_24A_1.1.fq.gz 1SN_25A_1.1.fq.gz 1SN_26A_1.1.fq.gz 1SN_27A_1.1.fq.gz 1SN_28A_1.1.fq.gz 1SN_29A_1.1.fq.gz 1SN_2A_1.1.fq.gz 1SN_30A_1.1.fq.gz 1SN_31A_1.1.fq.gz 1SN_32A_1.1.fq.gz 1SN_3A_1.1.fq.gz 1SN_4A_1.1.fq.gz 1SN_5A_1.1.fq.gz 1SN_6A_1.1.fq.gz 1SN_7A_1.1.fq.gz 1SN_8A_1.1.fq.gz 1SN_9A_1.1.fq.gz )
list2=( 1HL_10A_1.rem.1.fq.gz 1HL_11A_1.rem.1.fq.gz 1HL_12A_1.rem.1.fq.gz 1HL_13A_1.rem.1.fq.gz 1HL_14A_1.rem.1.fq.gz 1HL_15A_1.rem.1.fq.gz 1HL_16A_1.rem.1.fq.gz 1HL_17A_1.rem.1.fq.gz 1HL_19A_1.rem.1.fq.gz 1HL_1A_1.rem.1.fq.gz 1HL_20A_1.rem.1.fq.gz 1HL_21A_1.rem.1.fq.gz 1HL_22A_1.rem.1.fq.gz 1HL_23A_1.rem.1.fq.gz 1HL_24A_1.rem.1.fq.gz 1HL_25A_1.rem.1.fq.gz 1HL_26A_1.rem.1.fq.gz 1HL_27A_1.rem.1.fq.gz 1HL_28A_1.rem.1.fq.gz 1HL_29A_1.rem.1.fq.gz 1HL_2A_1.rem.1.fq.gz 1HL_31A_1.rem.1.fq.gz 1HL_33A_1.rem.1.fq.gz 1HL_34A_1.rem.1.fq.gz 1HL_35A_1.rem.1.fq.gz 1HL_3A_1.rem.1.fq.gz 1HL_4A_1.rem.1.fq.gz 1HL_5A_1.rem.1.fq.gz 1HL_6A_1.rem.1.fq.gz 1HL_7A_1.rem.1.fq.gz 1HL_8A_1.rem.1.fq.gz 1HL_9A_1.rem.1.fq.gz 1NF_10A_1.rem.1.fq.gz 1NF_11A_1.rem.1.fq.gz 1NF_12A_1.rem.1.fq.gz 1NF_13A_1.rem.1.fq.gz 1NF_14A_1.rem.1.fq.gz 1NF_15A_1.rem.1.fq.gz 1NF_16A_1.rem.1.fq.gz 1NF_17A_1.rem.1.fq.gz 1NF_18A_1.rem.1.fq.gz 1NF_19A_1.rem.1.fq.gz 1NF_1A_1.rem.1.fq.gz 1NF_20A_1.rem.1.fq.gz 1NF_21A_1.rem.1.fq.gz 1NF_22A_1.rem.1.fq.gz 1NF_23A_1.rem.1.fq.gz 1NF_24A_1.rem.1.fq.gz 1NF_25A_1.rem.1.fq.gz 1NF_26A_1.rem.1.fq.gz 1NF_27A_1.rem.1.fq.gz 1NF_28A_1.rem.1.fq.gz 1NF_29A_1.rem.1.fq.gz 1NF_2A_1.rem.1.fq.gz 1NF_30A_1.rem.1.fq.gz 1NF_31A_1.rem.1.fq.gz 1NF_32A_1.rem.1.fq.gz 1NF_33A_1.rem.1.fq.gz 1NF_4A_1.rem.1.fq.gz 1NF_5A_1.rem.1.fq.gz 1NF_6A_1.rem.1.fq.gz 1NF_7A_1.rem.1.fq.gz 1NF_8A_1.rem.1.fq.gz 1NF_9A_1.rem.1.fq.gz 1SN_10A_1.rem.1.fq.gz 1SN_11A_1.rem.1.fq.gz 1SN_12A_1.rem.1.fq.gz 1SN_13A_1.rem.1.fq.gz 1SN_14A_1.rem.1.fq.gz 1SN_15A_1.rem.1.fq.gz 1SN_16A_1.rem.1.fq.gz 1SN_17A_1.rem.1.fq.gz 1SN_18A_1.rem.1.fq.gz 1SN_19A_1.rem.1.fq.gz 1SN_1A_1.rem.1.fq.gz 1SN_20A_1.rem.1.fq.gz 1SN_21A_1.rem.1.fq.gz 1SN_22A_1.rem.1.fq.gz 1SN_23A_1.rem.1.fq.gz 1SN_24A_1.rem.1.fq.gz 1SN_25A_1.rem.1.fq.gz 1SN_26A_1.rem.1.fq.gz 1SN_27A_1.rem.1.fq.gz 1SN_28A_1.rem.1.fq.gz 1SN_29A_1.rem.1.fq.gz 1SN_2A_1.rem.1.fq.gz 1SN_30A_1.rem.1.fq.gz 1SN_31A_1.rem.1.fq.gz 1SN_32A_1.rem.1.fq.gz 1SN_3A_1.rem.1.fq.gz 1SN_4A_1.rem.1.fq.gz 1SN_5A_1.rem.1.fq.gz 1SN_6A_1.rem.1.fq.gz 1SN_7A_1.rem.1.fq.gz 1SN_8A_1.rem.1.fq.gz 1SN_9A_1.rem.1.fq.gz )
list3=( 1HL_10A_2.2.fq.gz 1HL_11A_2.2.fq.gz 1HL_12A_2.2.fq.gz 1HL_13A_2.2.fq.gz 1HL_14A_2.2.fq.gz 1HL_15A_2.2.fq.gz 1HL_16A_2.2.fq.gz 1HL_17A_2.2.fq.gz 1HL_19A_2.2.fq.gz 1HL_1A_2.2.fq.gz 1HL_20A_2.2.fq.gz 1HL_21A_2.2.fq.gz 1HL_22A_2.2.fq.gz 1HL_23A_2.2.fq.gz 1HL_24A_2.2.fq.gz 1HL_25A_2.2.fq.gz 1HL_26A_2.2.fq.gz 1HL_27A_2.2.fq.gz 1HL_28A_2.2.fq.gz 1HL_29A_2.2.fq.gz 1HL_2A_2.2.fq.gz 1HL_31A_2.2.fq.gz 1HL_33A_2.2.fq.gz 1HL_34A_2.2.fq.gz 1HL_35A_2.2.fq.gz 1HL_3A_2.2.fq.gz 1HL_4A_2.2.fq.gz 1HL_5A_2.2.fq.gz 1HL_6A_2.2.fq.gz 1HL_7A_2.2.fq.gz 1HL_8A_2.2.fq.gz 1HL_9A_2.2.fq.gz 1NF_10A_2.2.fq.gz 1NF_11A_2.2.fq.gz 1NF_12A_2.2.fq.gz 1NF_13A_2.2.fq.gz 1NF_14A_2.2.fq.gz 1NF_15A_2.2.fq.gz 1NF_16A_2.2.fq.gz 1NF_17A_2.2.fq.gz 1NF_18A_2.2.fq.gz 1NF_19A_2.2.fq.gz 1NF_1A_2.2.fq.gz 1NF_20A_2.2.fq.gz 1NF_21A_2.2.fq.gz 1NF_22A_2.2.fq.gz 1NF_23A_2.2.fq.gz 1NF_24A_2.2.fq.gz 1NF_25A_2.2.fq.gz 1NF_26A_2.2.fq.gz 1NF_27A_2.2.fq.gz 1NF_28A_2.2.fq.gz 1NF_29A_2.2.fq.gz 1NF_2A_2.2.fq.gz 1NF_30A_2.2.fq.gz 1NF_31A_2.2.fq.gz 1NF_32A_2.2.fq.gz 1NF_33A_2.2.fq.gz 1NF_4A_2.2.fq.gz 1NF_5A_2.2.fq.gz 1NF_6A_2.2.fq.gz 1NF_7A_2.2.fq.gz 1NF_8A_2.2.fq.gz 1NF_9A_2.2.fq.gz 1SN_10A_2.2.fq.gz 1SN_11A_2.2.fq.gz 1SN_12A_2.2.fq.gz 1SN_13A_2.2.fq.gz 1SN_14A_2.2.fq.gz 1SN_15A_2.2.fq.gz 1SN_16A_2.2.fq.gz 1SN_17A_2.2.fq.gz 1SN_18A_2.2.fq.gz 1SN_19A_2.2.fq.gz 1SN_1A_2.2.fq.gz 1SN_20A_2.2.fq.gz 1SN_21A_2.2.fq.gz 1SN_22A_2.2.fq.gz 1SN_23A_2.2.fq.gz 1SN_24A_2.2.fq.gz 1SN_25A_2.2.fq.gz 1SN_26A_2.2.fq.gz 1SN_27A_2.2.fq.gz 1SN_28A_2.2.fq.gz 1SN_29A_2.2.fq.gz 1SN_2A_2.2.fq.gz 1SN_30A_2.2.fq.gz 1SN_31A_2.2.fq.gz 1SN_32A_2.2.fq.gz 1SN_3A_2.2.fq.gz 1SN_4A_2.2.fq.gz 1SN_5A_2.2.fq.gz 1SN_6A_2.2.fq.gz 1SN_7A_2.2.fq.gz 1SN_8A_2.2.fq.gz 1SN_9A_2.2.fq.gz )
list4=( 1HL_10A_2.rem.2.fq.gz 1HL_11A_2.rem.2.fq.gz 1HL_12A_2.rem.2.fq.gz 1HL_13A_2.rem.2.fq.gz 1HL_14A_2.rem.2.fq.gz 1HL_15A_2.rem.2.fq.gz 1HL_16A_2.rem.2.fq.gz 1HL_17A_2.rem.2.fq.gz 1HL_19A_2.rem.2.fq.gz 1HL_1A_2.rem.2.fq.gz 1HL_20A_2.rem.2.fq.gz 1HL_21A_2.rem.2.fq.gz 1HL_22A_2.rem.2.fq.gz 1HL_23A_2.rem.2.fq.gz 1HL_24A_2.rem.2.fq.gz 1HL_25A_2.rem.2.fq.gz 1HL_26A_2.rem.2.fq.gz 1HL_27A_2.rem.2.fq.gz 1HL_28A_2.rem.2.fq.gz 1HL_29A_2.rem.2.fq.gz 1HL_2A_2.rem.2.fq.gz 1HL_31A_2.rem.2.fq.gz 1HL_33A_2.rem.2.fq.gz 1HL_34A_2.rem.2.fq.gz 1HL_35A_2.rem.2.fq.gz 1HL_3A_2.rem.2.fq.gz 1HL_4A_2.rem.2.fq.gz 1HL_5A_2.rem.2.fq.gz 1HL_6A_2.rem.2.fq.gz 1HL_7A_2.rem.2.fq.gz 1HL_8A_2.rem.2.fq.gz 1HL_9A_2.rem.2.fq.gz 1NF_10A_2.rem.2.fq.gz 1NF_11A_2.rem.2.fq.gz 1NF_12A_2.rem.2.fq.gz 1NF_13A_2.rem.2.fq.gz 1NF_14A_2.rem.2.fq.gz 1NF_15A_2.rem.2.fq.gz 1NF_16A_2.rem.2.fq.gz 1NF_17A_2.rem.2.fq.gz 1NF_18A_2.rem.2.fq.gz 1NF_19A_2.rem.2.fq.gz 1NF_1A_2.rem.2.fq.gz 1NF_20A_2.rem.2.fq.gz 1NF_21A_2.rem.2.fq.gz 1NF_22A_2.rem.2.fq.gz 1NF_23A_2.rem.2.fq.gz 1NF_24A_2.rem.2.fq.gz 1NF_25A_2.rem.2.fq.gz 1NF_26A_2.rem.2.fq.gz 1NF_27A_2.rem.2.fq.gz 1NF_28A_2.rem.2.fq.gz 1NF_29A_2.rem.2.fq.gz 1NF_2A_2.rem.2.fq.gz 1NF_30A_2.rem.2.fq.gz 1NF_31A_2.rem.2.fq.gz 1NF_32A_2.rem.2.fq.gz 1NF_33A_2.rem.2.fq.gz 1NF_4A_2.rem.2.fq.gz 1NF_5A_2.rem.2.fq.gz 1NF_6A_2.rem.2.fq.gz 1NF_7A_2.rem.2.fq.gz 1NF_8A_2.rem.2.fq.gz 1NF_9A_2.rem.2.fq.gz 1SN_10A_2.rem.2.fq.gz 1SN_11A_2.rem.2.fq.gz 1SN_12A_2.rem.2.fq.gz 1SN_13A_2.rem.2.fq.gz 1SN_14A_2.rem.2.fq.gz 1SN_15A_2.rem.2.fq.gz 1SN_16A_2.rem.2.fq.gz 1SN_17A_2.rem.2.fq.gz 1SN_18A_2.rem.2.fq.gz 1SN_19A_2.rem.2.fq.gz 1SN_1A_2.rem.2.fq.gz 1SN_20A_2.rem.2.fq.gz 1SN_21A_2.rem.2.fq.gz 1SN_22A_2.rem.2.fq.gz 1SN_23A_2.rem.2.fq.gz 1SN_24A_2.rem.2.fq.gz 1SN_25A_2.rem.2.fq.gz 1SN_26A_2.rem.2.fq.gz 1SN_27A_2.rem.2.fq.gz 1SN_28A_2.rem.2.fq.gz 1SN_29A_2.rem.2.fq.gz 1SN_2A_2.rem.2.fq.gz 1SN_30A_2.rem.2.fq.gz 1SN_31A_2.rem.2.fq.gz 1SN_32A_2.rem.2.fq.gz 1SN_3A_2.rem.2.fq.gz 1SN_4A_2.rem.2.fq.gz 1SN_5A_2.rem.2.fq.gz 1SN_6A_2.rem.2.fq.gz 1SN_7A_2.rem.2.fq.gz 1SN_8A_2.rem.2.fq.gz 1SN_9A_2.rem.2.fq.gz )

time for index in "${!list1[@]}"; do
  i=${list1[$index]}
  j=${list2[$index]}
  k=${list3[$index]}
  l=${list4[$index]}
  cat $i $j $k $l > ${i/_1.1/}
  
done

real	22m35.250s
user	0m2.167s
sys	1m28.419s

In [26]:

%%bash
echo *A.fq.gz

1HL_10A.fq.gz 1HL_11A.fq.gz 1HL_12A.fq.gz 1HL_13A.fq.gz 1HL_14A.fq.gz 1HL_15A.fq.gz 1HL_16A.fq.gz 1HL_17A.fq.gz 1HL_19A.fq.gz 1HL_1A.fq.gz 1HL_20A.fq.gz 1HL_21A.fq.gz 1HL_22A.fq.gz 1HL_23A.fq.gz 1HL_24A.fq.gz 1HL_25A.fq.gz 1HL_26A.fq.gz 1HL_27A.fq.gz 1HL_28A.fq.gz 1HL_29A.fq.gz 1HL_2A.fq.gz 1HL_31A.fq.gz 1HL_33A.fq.gz 1HL_34A.fq.gz 1HL_35A.fq.gz 1HL_3A.fq.gz 1HL_4A.fq.gz 1HL_5A.fq.gz 1HL_6A.fq.gz 1HL_7A.fq.gz 1HL_8A.fq.gz 1HL_9A.fq.gz 1NF_10A.fq.gz 1NF_11A.fq.gz 1NF_12A.fq.gz 1NF_13A.fq.gz 1NF_14A.fq.gz 1NF_15A.fq.gz 1NF_16A.fq.gz 1NF_17A.fq.gz 1NF_18A.fq.gz 1NF_19A.fq.gz 1NF_1A.fq.gz 1NF_20A.fq.gz 1NF_21A.fq.gz 1NF_22A.fq.gz 1NF_23A.fq.gz 1NF_24A.fq.gz 1NF_25A.fq.gz 1NF_26A.fq.gz 1NF_27A.fq.gz 1NF_28A.fq.gz 1NF_29A.fq.gz 1NF_2A.fq.gz 1NF_30A.fq.gz 1NF_31A.fq.gz 1NF_32A.fq.gz 1NF_33A.fq.gz 1NF_4A.fq.gz 1NF_5A.fq.gz 1NF_6A.fq.gz 1NF_7A.fq.gz 1NF_8A.fq.gz 1NF_9A.fq.gz 1SN_10A.fq.gz 1SN_11A.fq.gz 1SN_12A.fq.gz 1SN_13A.fq.gz 1SN_14A.fq.gz 1SN_15A.fq.gz 1SN_16A.fq.gz 1SN_17A.fq.gz 1SN_18A.fq.gz 1SN_19A.fq.gz 1SN_1A.fq.gz 1SN_20A.fq.gz 1SN_21A.fq.gz 1SN_22A.fq.gz 1SN_23A.fq.gz 1SN_24A.fq.gz 1SN_25A.fq.gz 1SN_26A.fq.gz 1SN_27A.fq.gz 1SN_28A.fq.gz 1SN_29A.fq.gz 1SN_2A.fq.gz 1SN_30A.fq.gz 1SN_31A.fq.gz 1SN_32A.fq.gz 1SN_3A.fq.gz 1SN_4A.fq.gz 1SN_5A.fq.gz 1SN_6A.fq.gz 1SN_7A.fq.gz 1SN_8A.fq.gz 1SN_9A.fq.gz

In [ ]:

%%bash
#Runs ustacks and appends sql ID to each file for downstream analysis.
sql_id=0
time for i in *A.fq.gz; do
  ((sql_id++))
  /usr/local/bioinformatics/stacks-1.37/ustacks \
  -t gzfastq \
  -f $i \
  -o /Volumes/toaster/sam/scratch/20160428_Oly_GBS_stacks/stacks/ \
  -i $sql_id \
  -d \
  -r \
  -p 16
done

The command above continually failed with a segmentation fault 11 error. Additionally, the external HDD this operation was reading/writing to became unresponsive on 5/4/2016. Will proceed with whatever data has been completed for this analysis.¶

List file names and format for subsequent use in cstacks command¶

In [1]:

cd /Volumes/toaster/sam/scratch/20160428_Oly_GBS_stacks/stacks/

/Volumes/toaster/sam/scratch/20160428_Oly_GBS_stacks/stacks

In [2]:

%%bash
#Uses printf statement to print just the first part of each filename, without the extension, and ads a "-s" and a " \"
#to each line for use in the subsequent cstacks command.
for fname in *; do printf " %s\n" "-s ${fname%%.*} \\" >> tmp.txt; done
cat tmp.txt | uniq
rm tmp.txt

 -s 1HL_10A \
 -s 1HL_11A \
 -s 1HL_12A \
 -s 1HL_13A \
 -s 1HL_14A \
 -s 1HL_15A \
 -s 1HL_16A \
 -s 1HL_17A \
 -s 1HL_19A \
 -s 1HL_1A \
 -s 1HL_20A \
 -s 1HL_21A \
 -s 1HL_22A \
 -s 1HL_23A \
 -s 1HL_24A \
 -s 1HL_25A \
 -s 1HL_26A \
 -s 1HL_27A \
 -s 1HL_28A \
 -s 1HL_29A \
 -s 1HL_2A \
 -s 1HL_31A \
 -s 1HL_33A \
 -s 1HL_34A \
 -s 1HL_35A \
 -s 1HL_3A \
 -s 1HL_4A \
 -s 1HL_5A \
 -s 1HL_6A \
 -s 1HL_7A \
 -s 1HL_8A \
 -s 1HL_9A \
 -s 1NF_10A \
 -s 1NF_11A \
 -s 1NF_12A \
 -s 1NF_13A \
 -s 1NF_14A \
 -s 1NF_15A \
 -s 1NF_16A \
 -s 1NF_17A \
 -s 1NF_18A \
 -s 1NF_19A \
 -s 1NF_1A \
 -s 1NF_20A \
 -s 1NF_21A \
 -s 1NF_22A \
 -s 1NF_23A \
 -s 1NF_24A \
 -s 1NF_25A \
 -s 1NF_26A \
 -s 1NF_27A \
 -s 1NF_28A \
 -s 1NF_29A \
 -s 1NF_2A \
 -s 1NF_30A \
 -s 1NF_31A \
 -s 1NF_32A \
 -s 1NF_33A \
 -s 1NF_4A \
 -s 1NF_5A \
 -s 1NF_6A \
 -s 1NF_7A \
 -s 1NF_8A \
 -s 1NF_9A \
 -s 1SN_10A \
 -s 1SN_11A \
 -s 1SN_12A \
 -s 1SN_13A \
 -s 1SN_14A \
 -s 1SN_15A \
 -s 1SN_16A \
 -s 1SN_17A \
 -s 1SN_18A \
 -s 1SN_19A \
 -s 1SN_1A \
 -s 1SN_20A \
 -s 1SN_21A \
 -s 1SN_22A \
 -s 1SN_23A \
 -s 1SN_24A \
 -s 1SN_25A \
 -s 1SN_26A \
 -s 1SN_27A \
 -s 1SN_28A \
 -s 1SN_29A \
 -s 1SN_2A \
 -s 1SN_30A \
 -s 1SN_31A \
 -s 1SN_32A \
 -s 1SN_3A \

In [3]:

%%bash
#cstacks command.
time /usr/local/bioinformatics/stacks-1.37/cstacks -b 1 -o . \
-p 16 \
 -s 1HL_10A \
 -s 1HL_11A \
 -s 1HL_12A \
 -s 1HL_13A \
 -s 1HL_14A \
 -s 1HL_15A \
 -s 1HL_16A \
 -s 1HL_17A \
 -s 1HL_19A \
 -s 1HL_1A \
 -s 1HL_20A \
 -s 1HL_21A \
 -s 1HL_22A \
 -s 1HL_23A \
 -s 1HL_24A \
 -s 1HL_25A \
 -s 1HL_26A \
 -s 1HL_27A \
 -s 1HL_28A \
 -s 1HL_29A \
 -s 1HL_2A \
 -s 1HL_31A \
 -s 1HL_33A \
 -s 1HL_34A \
 -s 1HL_35A \
 -s 1HL_3A \
 -s 1HL_4A \
 -s 1HL_5A \
 -s 1HL_6A \
 -s 1HL_7A \
 -s 1HL_8A \
 -s 1HL_9A \
 -s 1NF_10A \
 -s 1NF_11A \
 -s 1NF_12A \
 -s 1NF_13A \
 -s 1NF_14A \
 -s 1NF_15A \
 -s 1NF_16A \
 -s 1NF_17A \
 -s 1NF_18A \
 -s 1NF_19A \
 -s 1NF_1A \
 -s 1NF_20A \
 -s 1NF_21A \
 -s 1NF_22A \
 -s 1NF_23A \
 -s 1NF_24A \
 -s 1NF_25A \
 -s 1NF_26A \
 -s 1NF_27A \
 -s 1NF_28A \
 -s 1NF_29A \
 -s 1NF_2A \
 -s 1NF_30A \
 -s 1NF_31A \
 -s 1NF_32A \
 -s 1NF_33A \
 -s 1NF_4A \
 -s 1NF_5A \
 -s 1NF_6A \
 -s 1NF_7A \
 -s 1NF_8A \
 -s 1NF_9A \
 -s 1SN_10A \
 -s 1SN_11A \
 -s 1SN_12A \
 -s 1SN_13A \
 -s 1SN_14A \
 -s 1SN_15A \
 -s 1SN_16A \
 -s 1SN_17A \
 -s 1SN_18A \
 -s 1SN_19A \
 -s 1SN_1A \
 -s 1SN_20A \
 -s 1SN_21A \
 -s 1SN_22A \
 -s 1SN_23A \
 -s 1SN_24A \
 -s 1SN_25A \
 -s 1SN_26A \
 -s 1SN_27A \
 -s 1SN_28A \
 -s 1SN_29A \
 -s 1SN_2A \
 -s 1SN_30A \
 -s 1SN_31A \
 -s 1SN_32A \
 -s 1SN_3A

Number of mismatches allowed between stacks: 1
Loci matched based on sequence identity.
Constructing catalog from 90 samples.
Initializing new catalog...
  Parsing 1HL_10A.tags.tsv.gz
  Parsing 1HL_10A.snps.tsv.gz
  Parsing 1HL_10A.alleles.tsv.gz
Processing sample 1HL_10A [2 of 90]
  Parsing 1HL_11A.tags.tsv.gz
  Parsing 1HL_11A.snps.tsv.gz
  Parsing 1HL_11A.alleles.tsv.gz
Searching for sequence matches...
  Distance allowed between stacks: 1
  Using a k-mer length of 49
  Number of kmers per sequence: 52
  Minimum number of k-mers to define a match: 3
  206709 loci in the catalog, 9475033 kmers in the catalog hash.
Merging matches into catalog...
  19048 loci matched more than one catalog locus and were excluded.
Processing sample 1HL_11A [3 of 90]
  Parsing 1HL_12A.tags.tsv.gz
  Parsing 1HL_12A.snps.tsv.gz
  Parsing 1HL_12A.alleles.tsv.gz
Searching for sequence matches...
  Distance allowed between stacks: 1
  Using a k-mer length of 49
  Number of kmers per sequence: 52
  Minimum number of k-mers to define a match: 3
  304949 loci in the catalog, 14156292 kmers in the catalog hash.
Merging matches into catalog...
  16397 loci matched more than one catalog locus and were excluded.
Processing sample 1HL_12A [4 of 90]
  Parsing 1HL_13A.tags.tsv.gz
  Parsing 1HL_13A.snps.tsv.gz
Error parsing 1HL_13A.snps.tsv.gz at line: 36196. SNP asks for nonexistent locus with ID: 116506
Failed to load sample 4
Processing sample 1HL_13A [4 of 90]
  Parsing 1HL_14A.tags.tsv.gz
  Parsing 1HL_14A.snps.tsv.gz
Error parsing 1HL_14A.snps.tsv.gz at line: 31291. SNP asks for nonexistent locus with ID: 116883
Failed to load sample 4
Processing sample 1HL_14A [4 of 90]
  Parsing 1HL_15A.tags.tsv.gz
  Parsing 1HL_15A.snps.tsv.gz
  Parsing 1HL_15A.alleles.tsv.gz
Searching for sequence matches...
  Distance allowed between stacks: 1
  Using a k-mer length of 49
  Number of kmers per sequence: 52
  Minimum number of k-mers to define a match: 3
  368906 loci in the catalog, 17317529 kmers in the catalog hash.
Merging matches into catalog...
  17807 loci matched more than one catalog locus and were excluded.
Processing sample 1HL_15A [5 of 90]
  Parsing 1HL_16A.tags.tsv.gz
  Parsing 1HL_16A.snps.tsv.gz
  Parsing 1HL_16A.alleles.tsv.gz
Searching for sequence matches...
bash: line 93: 83337 Segmentation fault: 11  /usr/local/bioinformatics/stacks-1.37/cstacks -b 1 -o . -p 16 -s 1HL_10A -s 1HL_11A -s 1HL_12A -s 1HL_13A -s 1HL_14A -s 1HL_15A -s 1HL_16A -s 1HL_17A -s 1HL_19A -s 1HL_1A -s 1HL_20A -s 1HL_21A -s 1HL_22A -s 1HL_23A -s 1HL_24A -s 1HL_25A -s 1HL_26A -s 1HL_27A -s 1HL_28A -s 1HL_29A -s 1HL_2A -s 1HL_31A -s 1HL_33A -s 1HL_34A -s 1HL_35A -s 1HL_3A -s 1HL_4A -s 1HL_5A -s 1HL_6A -s 1HL_7A -s 1HL_8A -s 1HL_9A -s 1NF_10A -s 1NF_11A -s 1NF_12A -s 1NF_13A -s 1NF_14A -s 1NF_15A -s 1NF_16A -s 1NF_17A -s 1NF_18A -s 1NF_19A -s 1NF_1A -s 1NF_20A -s 1NF_21A -s 1NF_22A -s 1NF_23A -s 1NF_24A -s 1NF_25A -s 1NF_26A -s 1NF_27A -s 1NF_28A -s 1NF_29A -s 1NF_2A -s 1NF_30A -s 1NF_31A -s 1NF_32A -s 1NF_33A -s 1NF_4A -s 1NF_5A -s 1NF_6A -s 1NF_7A -s 1NF_8A -s 1NF_9A -s 1SN_10A -s 1SN_11A -s 1SN_12A -s 1SN_13A -s 1SN_14A -s 1SN_15A -s 1SN_16A -s 1SN_17A -s 1SN_18A -s 1SN_19A -s 1SN_1A -s 1SN_20A -s 1SN_21A -s 1SN_22A -s 1SN_23A -s 1SN_24A -s 1SN_25A -s 1SN_26A -s 1SN_27A -s 1SN_28A -s 1SN_29A -s 1SN_2A -s 1SN_30A -s 1SN_31A -s 1SN_32A -s 1SN_3A

real	5m56.645s
user	5m44.765s
sys	0m10.503s

In [ ]:

Move to directory with GBS FASTQ files¶

List all FASTQ files for use in subsequent STACKS command¶

Run QC on files with process_radtags component¶

Cell below creates two lists (one list for each individual pair of FASTQs), loops through each as an array and assigns the corresponding FASTQ pairs to the variables "i" and "j". The values in "i" and "j" are used in the process_radtags command for matching the paired FASTQ files.¶

Concatenate process_radtags output files into single FASTQ file¶

Create four lists - each of the four output files generated per individual for use in subsequent concatenation command.¶

The command above continually failed with a segmentation fault 11 error. Additionally, the external HDD this operation was reading/writing to became unresponsive on 5/4/2016. Will proceed with whatever data has been completed for this analysis.¶

List file names and format for subsequent use in cstacks command¶

Run QC on files with `process_radtags` component¶

Cell below creates two lists (one list for each individual pair of FASTQs), loops through each as an array and assigns the corresponding FASTQ pairs to the variables "i" and "j". The values in "i" and "j" are used in the `process_radtags` command for matching the paired FASTQ files.¶

Concatenate `process_radtags` output files into single FASTQ file¶