I'm going to concatonate the Sept and Nov runs from my Larvae data (R1 and R2 separately)

F_R1

In [1]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgF_TTAGGC_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgF_TTAGGC_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/F_R1.fastq

M1_R1

In [2]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM1_ACTTGA_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM1_ACTTGA_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M1_R1.fastq

M3_R1

In [3]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM3_GATCAG_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM3_GATCAG_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/M3_R1.fastq

T1D3_R1

In [4]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T1D3_TGACCA_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T1D3_TGACCA_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D3_R1.fastq

T1D5_R1

In [5]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T1D5_ACAGTG_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R1.fastq >  /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T1D5_R1.fastq

T3D3_R1

In [6]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_Bs_CgLarve_T3D3_GCCAAT_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_Bs_CgLarve_T3D3_GCCAAT_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D3_R1.fastq

T3D5_R1

In [7]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T3D5_CAGATC_L004_R1.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T3D5_CAGATC_L007_R1.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R1/T3D5_R1.fastq

F_R2

In [8]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgF_TTAGGC_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgF_TTAGGC_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/F_R2.fastq

M1_R2

In [9]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM1_ACTTGA_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM1_ACTTGA_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M1_R2.fastq

M3_R2

In [10]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgM3_GATCAG_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgM3_GATCAG_L007_R2.fastq >  /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/M3_R2.fastq

T1D3_R2

In [11]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T1D3_TGACCA_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T1D3_TGACCA_L007_R2.fastq >  /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D3_R2.fastq

T1D5_R2

In [12]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T1D5_ACAGTG_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T1D5_ACAGTG_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T1D5_R2.fastq

T3D3_R2

In [13]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_Bs_CgLarve_T3D3_GCCAAT_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_Bs_CgLarve_T3D3_GCCAAT_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D3_R2.fastq

T3D5_R2

In [14]: 
!cat /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Nov/filtered_BS_CgLarv_T3D5_CAGATC_L004_R2.fastq /Volumes/web/Mollusk/bs_larvae_exp/Uncompressed_Sept/filtered_BS_CgLarv_T3D5_CAGATC_L007_R2.fastq > /Volumes/web/Mollusk/bs_larvae_exp/Concatenated_Files_R2/T3D5_R2.fastq
In []: