###################

#Lane 2 Ar_jam MOE#

###################

gunzip pair*

cat pair.DR004_Artibeus_Jamaicensis_MOE_ACAGTG_L002_R1* >> Arjam_MOE_L2_R1.fq

cat pair.DR004_Artibeus_Jamaicensis_MOE_ACAGTG_L002_R2* >> Arjam_MOE_L2_R2.fq

fastq_quality_filter -i Arjam_MOE_L2_R1.fq -o Arjam_MOE_R1_L2_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v

Quality cut-off: 20

Minimum percentage: 80

Input: 15317036 reads.

Output: 14847480 reads.

discarded 469556 (3%) low-quality reads.

fastq_quality_filter -i Arjam_MOE_L2_R2.fq -o Arjam_MOE_R2_L2_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v

Quality cut-off: 20

Minimum percentage: 80

Input: 15317036 reads.

Output: 14608448 reads.

discarded 708588 (4%) low-quality reads.

~/Scripts/both.py Arjam_MOE_R1_L2_fastxtrimmed.fastq Arjam_MOE_R2_L2_fastxtrimmed.fastq

#run trinity

Trinity.pl --seqType fq --left Arjam_MOE_R1_L2_fastxtrimmed.fastq.both --right Arjam_MOE_R2_L2_fastxtrimmed.fastq.both --CPU 4 --JM 20G --output output_Lane2

###################

#Lane 1 Ar_jam VNO#

###################

gunzip pair*

cat pair.DR011_Artibeus_Jamaicensis_VNO_TGACCA_L001_R1* >> Arjam_VNO_L1_R1.fq

cat pair.DR011_Artibeus_Jamaicensis_VNO_TGACCA_L001_R2* >> Arjam_VNO_L1_R2.fq

mv Arjam_VNO_L1_R* /Volumes/Spare/transcriptomes/MOE_VNO_transcriptomes/Trinity_assembly/to_assemble/DR_011_Arjam_VNO/

fastq_quality_filter -i Arjam_VNO_L1_R1.fq -o Arjam_VNO_R1_L1_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v

Quality cut-off: 20

Minimum percentage: 80

Input: 13582991 reads.

Output: 13087556 reads.

discarded 495435 (3%) low-quality reads.

fastq_quality_filter -i Arjam_VNO_L1_R2.fq -o Arjam_VNO_R2_L1_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v

Quality cut-off: 20

Minimum percentage: 80

Input: 13582991 reads.

Output: 12665813 reads.

discarded 917178 (6%) low-quality reads.

~/Scripts/both.py Arjam_VNO_R1_L1_fastxtrimmed.fastq Arjam_VNO_R2_L1_fastxtrimmed.fastq

Trinity.pl --seqType fq --left Arjam_VNO_R1_L1_fastxtrimmed.fastq.both --right Arjam_VNO_R2_L1_fastxtrimmed.fastq.both --CPU 4 --JM 20G --output output_Lane1

###################

#Lane 2 Ar_jam VNO#

###################

gunzip pair*

cat pair.DR011_Artibeus_Jamaicensis_VNO_TGACCA_L002_R1* >> Arjam_VNO_L2_R1.fq

cat pair.DR011_Artibeus_Jamaicensis_VNO_TGACCA_L002_R2* >> Arjam_VNO_L2_R2.fq

mv Arjam_VNO_L2_R* /Volumes/Spare/transcriptomes/MOE_VNO_transcriptomes/Trinity_assembly/to_assemble/DR_011_Arjam_VNO/

fastq_quality_filter -i Arjam_VNO_L2_R1.fq -o Arjam_VNO_R1_L2_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v

Quality cut-off: 20

Minimum percentage: 80

Input: 13746292 reads.

Output: 13242643 reads.

discarded 503649 (3%) low-quality reads.

fastq_quality_filter -i Arjam_VNO_L2_R2.fq -o Arjam_VNO_R2_L2_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v

Quality cut-off: 20

Minimum percentage: 80

Input: 13746292 reads.

Output: 12800383 reads.

discarded 945909 (6%) low-quality reads.

~/Scripts/both.py Arjam_VNO_R1_L2_fastxtrimmed.fastq Arjam_VNO_R2_L2_fastxtrimmed.fastq

Trinity.pl --seqType fq --left Arjam_VNO_R1_L2_fastxtrimmed.fastq.both --right Arjam_VNO_R2_L2_fastxtrimmed.fastq.both --CPU 4 --JM 20G --output output_Lane2

###################

#Lane 1 Mo_red MOE#

###################

gunzip pair*

cat pair.DR013_Monophyllus_Redmani_MOE_CAGATC_L001_R1* >> Mored_MOE_L1_R1.fq

cat pair.DR013_Monophyllus_Redmani_MOE_CAGATC_L001_R2* >> Mored_MOE_L1_R2.fq

mv Mored_MOE_L1_R* /Volumes/Spare/transcriptomes/MOE_VNO_transcriptomes/Trinity_assembly/to_assemble/DR_013_Mored_MOE/

fastq_quality_filter -i Mored_MOE_L1_R1.fq -o Mored_MOE_R1_L1_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v

Quality cut-off: 20

Minimum percentage: 80

Input: 14546140 reads.

Output: 14205942 reads.

discarded 340198 (2%) low-quality reads.

fastq_quality_filter -i Mored_MOE_L1_R2.fq -o Mored_MOE_R2_L1_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v

Quality cut-off: 20

Minimum percentage: 80

Input: 14546140 reads.

Output: 13998979 reads.

discarded 547161 (3%) low-quality reads.

~/Scripts/both.py Mored_MOE_R1_L1_fastxtrimmed.fastq Mored_MOE_R2_L1_fastxtrimmed.fastq

Trinity.pl --seqType fq --left Mored_MOE_R1_L1_fastxtrimmed.fastq.both --right Mored_MOE_R2_L1_fastxtrimmed.fastq.both --CPU 4 --JM 20G --output output_Lane1

###################

#Lane 2 Mo_red MOE#

###################

gunzip pair*

cat pair.DR013_Monophyllus_Redmani_MOE_CAGATC_L002_R1* >> Mored_MOE_L2_R1.fq

cat pair.DR013_Monophyllus_Redmani_MOE_CAGATC_L002_R2* >> Mored_MOE_L2_R2.fq

mv Mored_MOE_L2_R* /Volumes/Spare/transcriptomes/MOE_VNO_transcriptomes/Trinity_assembly/to_assemble/DR_013_Mored_MOE/

fastq_quality_filter -i Mored_MOE_L2_R1.fq -o Mored_MOE_R1_L2_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v

Quality cut-off: 20

Minimum percentage: 80

Input: 14719223 reads.

Output: 14370971 reads.

discarded 348252 (2%) low-quality reads.

fastq_quality_filter -i Mored_MOE_L2_R2.fq -o Mored_MOE_R2_L2_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v

Quality cut-off: 20

Minimum percentage: 80

Input: 14719223 reads.

Output: 14152391 reads.

discarded 566832 (3%) low-quality reads.

~/Scripts/both.py Mored_MOE_R1_L2_fastxtrimmed.fastq Mored_MOE_R2_L2_fastxtrimmed.fastq

Trinity.pl --seqType fq --left Mored_MOE_R1_L2_fastxtrimmed.fastq.both --right Mored_MOE_R2_L2_fastxtrimmed.fastq.both --CPU 4 --JM 20G --output output_Lane2

###################

#Lane 1 Mo_red VNO#

###################

gunzip pair*

cat pair.DR013_Monophyllus_Redmani_VNO_AGTCAA_L001_R1* >> Mored_VNO_L1_R1.fq

cat pair.DR013_Monophyllus_Redmani_VNO_AGTCAA_L001_R2* >> Mored_VNO_L1_R2.fq

mv Mored_VNO_L1_R* /Volumes/Spare/transcriptomes/MOE_VNO_transcriptomes/Trinity_assembly/to_assemble/DR_013_Mored_VNO/

fastq_quality_filter -i Mored_VNO_L1_R1.fq -o Mored_VNO_R1_L1_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v
Quality cut-off: 20
Minimum percentage: 80
Input: 14001874 reads.
Output: 13728472 reads.
discarded 273402 (1%) low-quality reads
fastq_quality_filter -i Mored_VNO_L1_R2.fq -o Mored_VNO_R2_L1_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v
Quality cut-off: 20
Minimum percentage: 80
Input: 14001874 reads.
Output: 13444029 reads.
discarded 557845 (3%) low-quality reads.

~/Scripts/both.py Mored_VNO_R1_L1_fastxtrimmed.fastq Mored_VNO_R2_L1_fastxtrimmed.fastq

Trinity.pl --seqType fq --left Mored_VNO_R1_L1_fastxtrimmed.fastq.both --right Mored_VNO_R2_L1_fastxtrimmed.fastq.both --CPU 4 --JM 20G --output output_Lane1

###################

#Lane 2 Mo_red VNO#

###################

gunzip pair*

cat pair.DR013_Monophyllus_Redmani_VNO_AGTCAA_L002_R1* >> Mored_VNO_L2_R1.fq

cat pair.DR013_Monophyllus_Redmani_VNO_AGTCAA_L002_R2* >> Mored_VNO_L2_R2.fq

mv Mored_VNO_L2_R* /Volumes/Spare/transcriptomes/MOE_VNO_transcriptomes/Trinity_assembly/to_assemble/DR_013_Mored_VNO/

fastq_quality_filter -i Mored_VNO_L2_R1.fq -o Mored_VNO_R1_L2_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v
Quality cut-off: 20
Minimum percentage: 80
Input: 14176309 reads.
Output: 13892340 reads.
discarded 283969 (2%) low-quality reads.
fastq_quality_filter -i Mored_VNO_L2_R2.fq -o Mored_VNO_R2_L2_fastxtrimmed.fastq -q 20 -p 80 -Q 33 
-v
Quality cut-off: 20
Minimum percentage: 80
Input: 14176309 reads.
Output: 13594457 reads.
discarded 581852 (4%) low-quality reads.

~/Scripts/both.py Mored_VNO_R1_L2_fastxtrimmed.fastq Mored_VNO_R2_L2_fastxtrimmed.fastq

Trinity.pl --seqType fq --left Mored_VNO_R1_L2_fastxtrimmed.fastq.both --right Mored_VNO_R2_L2_fastxtrimmed.fastq.both --CPU 4 --JM 20G --output output_Lane2

###################

#Lane 1 Mo_bla MOE#

###################

gunzip pair*

cat pair.DR091_Mormoops_Blainvelli_MOE_CGATGT_L001_R1* >> Mobla_MOE_L1_R1.fq

cat pair.DR091_Mormoops_Blainvelli_MOE_CGATGT_L001_R2* >> Mobla_MOE_L1_R2.fq

mv Mobla_MOE_L1_R* /Volumes/Spare/transcriptomes/MOE_VNO_transcriptomes/Trinity_assembly/to_assemble/DR_091_Mobl_MOE/

fastq_quality_filter -i Mobla_MOE_L1_R1.fq -o Mobl_MOE_R1_L1_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v
Quality cut-off: 20
Minimum percentage: 80
Input: 16080335 reads.
Output: 15736163 reads.

discarded 344172 (2%) low-quality reads.
fastq_quality_filter -i Mobla_MOE_L1_R2.fq -o Mobl_MOE_R2_L1_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v
Quality cut-off: 20
Minimum percentage: 80
Input: 16080335 reads.
Output: 15462533 reads.

discarded 617802 (3%) low-quality reads.

~/Scripts/both.py Mobl_MOE_R1_L1_fastxtrimmed.fastq Mobl_MOE_R2_L1_fastxtrimmed.fastq

Trinity.pl --seqType fq --left Mobl_MOE_R1_L1_fastxtrimmed.fastq.both --right Mobl_MOE_R2_L1_fastxtrimmed.fastq.both --CPU 4 --JM 20G --output output_Lane1

###################

#Lane 2 Mo_bla MOE#

###################

gunzip pair*

cat pair.DR091_Mormoops_Blainvelli_MOE_CGATGT_L002_R1* >> Mobla_MOE_L2_R1.fq

cat pair.DR091_Mormoops_Blainvelli_MOE_CGATGT_L002_R2* >> Mobla_MOE_L2_R2.fq

mv Mobla_MOE_L2_R* /Volumes/Spare/transcriptomes/MOE_VNO_transcriptomes/Trinity_assembly/to_assemble/DR_091_Mobl_MOE/

fastq_quality_filter -i Mobla_MOE_L2_R1.fq -o Mobl_MOE_R1_L2_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v
Quality cut-off: 20
Minimum percentage: 80
Input: 16263150 reads.
Output: 15909002 reads.

discarded 354148 (2%) low-quality reads.
fastq_quality_filter -i Mobla_MOE_L2_R2.fq -o Mobl_MOE_R2_L2_fastxtrimmed.fastq -q 20 -p 80 -Q 33 -v
Quality cut-off: 20
Minimum percentage: 80
Input: 16263150 reads.
Output: 15621798 reads.

discarded 641352 (3%) low-quality reads.

~/Scripts/both.py Mobl_MOE_R1_L2_fastxtrimmed.fastq Mobl_MOE_R2_L2_fastxtrimmed.fastq

Trinity.pl --seqType fq --left Mobl_MOE_R1_L2_fastxtrimmed.fastq.both --right Mobl_MOE_R2_L2_fastxtrimmed.fastq.both --CPU 4 --JM 20G --output output_Lane2