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trim.mk
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trim.mk
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#!/usr/bin/make -rRsf
MEM=5
TRIM=5
CPU=5
RUN=run
READ1=left.fastq
READ2=right.fastq
TRIMMOMATIC ?= $(shell which 'trimmomatic-0.30.jar')
BCODES := /home/macmanes/Dropbox/barcodes.fa
SOLEXA := /home/macmanes/software/
TRINITY := /home/macmanes/trinityrnaseq-code/trunk
MUS := /media/macmanes/hd/flux/genomes/mus/Mus_musculus.GRCm38.71.cdna.all.fa
PFAM := /media/macmanes/hd2/pfam/Pfam-A.hmm
subsamp10:raw.10M.$(READ1) raw.10M.$(READ2)
trim10:10M.left.0.fq 10M.left.0.fq 10M.left.2.fq 10M.left.5.fq 10M.left.10.fq 10M.left.20.fq 10M.right.2.fq 10M.right.5.fq 10M.right.10.fq 10M.right.20.fq
trin10:10M.0.Trinity.fasta 10M.2.Trinity.fasta 10M.5.Trinity.fasta 10M.10.Trinity.fasta 10M.20.Trinity.fasta raw.10M.Trinity.fasta \
10M.0.Trinity.fasta.pslx 10M.2.Trinity.fasta.pslx 10M.5.Trinity.fasta.pslx 10M.10.Trinity.fasta.pslx 10M.20.Trinity.fasta.pslx raw.10M.Trinity.fasta.pslx \
10M.0.Trinity.fasta.pep 10M.2.Trinity.fasta.pep 10M.5.Trinity.fasta.pep 10M.10.Trinity.fasta.pep 10M.20.Trinity.fasta.pep raw.10M.Trinity.fasta.pep \
10M.0.xprs 10M.2.xprs 10M.5.xprs 10M.10.xprs 10M.20.xprs raw.10M.xprs
subsamp20:raw.20M.$(READ1) raw.20M.$(READ2)
trim20:20M.left.0.fq 20M.left.0.fq 20M.left.2.fq 20M.left.5.fq 20M.left.10.fq 20M.left.20.fq 20M.right.2.fq 20M.right.5.fq 20M.right.10.fq 20M.right.20.fq
trin20:20M.0.Trinity.fasta 20M.2.Trinity.fasta 20M.5.Trinity.fasta 20M.10.Trinity.fasta 20M.20.Trinity.fasta raw.20M.Trinity.fasta \
20M.0.Trinity.fasta.pslx 20M.2.Trinity.fasta.pslx 20M.5.Trinity.fasta.pslx 20M.10.Trinity.fasta.pslx 20M.20.Trinity.fasta.pslx raw.20M.Trinity.fasta.pslx \
20M.0.Trinity.fasta.pep 20M.2.Trinity.fasta.pep 20M.5.Trinity.fasta.pep 20M.10.Trinity.fasta.pep 20M.20.Trinity.fasta.pep raw.20M.Trinity.fasta.pep \
20M.0.xprs 20M.2.xprs 20M.5.xprs 20M.10.xprs 20M.20.xprs raw.20M.xprs
subsamp50:raw.50M.$(READ1) raw.50M.$(READ2)
trim50:50M.left.0.fq 50M.left.0.fq 50M.left.2.fq 50M.left.5.fq 50M.left.10.fq 50M.left.20.fq 50M.right.2.fq 50M.right.5.fq 50M.right.10.fq 50M.right.20.fq
trin50:50M.0.Trinity.fasta 50M.2.Trinity.fasta 50M.5.Trinity.fasta 50M.10.Trinity.fasta 50M.20.Trinity.fasta raw.50M.Trinity.fasta \
50M.0.Trinity.fasta.pslx 50M.2.Trinity.fasta.pslx 50M.5.Trinity.fasta.pslx 50M.10.Trinity.fasta.pslx 50M.20.Trinity.fasta.pslx raw.50M.Trinity.fasta.pslx \
50M.0.Trinity.fasta.pep 50M.2.Trinity.fasta.pep 50M.5.Trinity.fasta.pep 50M.10.Trinity.fasta.pep 50M.20.Trinity.fasta.pep raw.50M.Trinity.fasta.pep \
50M.0.xprs 50M.2.xprs 50M.5.xprs 50M.10.xprs 50M.20.xprs raw.50M.xprs
subsamp75:raw.75M.$(READ1) raw.75M.$(READ2)
trim75:75M.left.0.fq 75M.left.0.fq 75M.left.2.fq 75M.left.5.fq 75M.left.10.fq 75M.left.20.fq 75M.right.2.fq 75M.right.5.fq 75M.right.10.fq 75M.right.20.fq
trin75:75M.0.Trinity.fasta 75M.2.Trinity.fasta 75M.5.Trinity.fasta 75M.10.Trinity.fasta 75M.20.Trinity.fasta raw.75M.Trinity.fasta \
75M.0.Trinity.fasta.pslx 75M.2.Trinity.fasta.pslx 75M.5.Trinity.fasta.pslx 75M.10.Trinity.fasta.pslx 75M.20.Trinity.fasta.pslx raw.75M.Trinity.fasta.pslx \
75M.0.Trinity.fasta.pep 75M.2.Trinity.fasta.pep 75M.5.Trinity.fasta.pep 75M.10.Trinity.fasta.pep 75M.20.Trinity.fasta.pep raw.75M.Trinity.fasta.pep \
75M.0.xprs 75M.2.xprs 75M.5.xprs 75M.10.xprs 75M.20.xprs raw.75M.xprs
subsamp100:raw.100M.$(READ1) raw.100M.$(READ2)
trim100:100M.left.0.fq 100M.left.0.fq 100M.left.2.fq 100M.left.5.fq 100M.left.10.fq 100M.left.20.fq 100M.right.2.fq 100M.right.5.fq 100M.right.10.fq 100M.right.20.fq
trin100:100M.0.Trinity.fasta 100M.2.Trinity.fasta 100M.5.Trinity.fasta 100M.10.Trinity.fasta 100M.20.Trinity.fasta raw.100M.Trinity.fasta \
100M.0.Trinity.fasta.pslx 100M.2.Trinity.fasta.pslx 100M.5.Trinity.fasta.pslx 100M.10.Trinity.fasta.pslx 100M.20.Trinity.fasta.pslx raw.100M.Trinity.fasta.pslx \
100M.0.Trinity.fasta.pep 100M.2.Trinity.fasta.pep 100M.5.Trinity.fasta.pep 100M.10.Trinity.fasta.pep 100M.20.Trinity.fasta.pep raw.100M.Trinity.fasta.pep \
100M.0.xprs 100M.2.xprs 100M.5.xprs 100M.10.xprs 100M.20.xprs raw.100M.xprs
$(READ1).quality: $(READ1) $(READ2)
perl $(SOLEXA)/SolexaQA.pl -p 0.01 $(READ1)
cp $(READ1).quality ~/Dropbox/
cp $(READ1).quality.pdf ~/Dropbox/
raw.10M.$(READ1) raw.10M.$(READ2):
python ~/error_correction/scripts/subsampler.py 10000000 $(READ1) $(READ2)
mv subsamp_1.fastq raw.10M.$(READ1)
mv subsamp_2.fastq raw.10M.$(READ2)
10M.left.2.fq 10M.left.5.fq 10M.left.10.fq 10M.left.20.fq 10M.right.2.fq 10M.right.5.fq 10M.right.10.fq 10M.right.20.fq:
@echo About to start trimming
for TRIM in 2 5 10 20 0; do \
java -Xmx$(MEM)g -jar $(TRIMMOMATIC) PE \
-phred33 -threads $(CPU) \
raw.10M.$(READ1) \
raw.10M.$(READ2) \
10M.$$TRIM.pp.1.fq \
10M.$$TRIM.up.1.fq \
10M.$$TRIM.pp.2.fq \
10M.$$TRIM.up.2.fq \
ILLUMINACLIP:$(BCODES):2:40:15 \
LEADING:$$TRIM \
TRAILING:$$TRIM \
SLIDINGWINDOW:4:$$TRIM \
MINLEN:25 1>> trim10.log; \
cat 10M.$$TRIM.pp.1.fq 10M.$$TRIM.up.1.fq > 10M.left.$$TRIM.fq ; \
cat 10M.$$TRIM.pp.2.fq 10M.$$TRIM.up.2.fq > 10M.right.$$TRIM.fq ; \
rm 10M.$$TRIM.pp.2.fq 10M.$$TRIM.up.2.fq 10M.$$TRIM.pp.1.fq 10M.$$TRIM.up.1.fq ; done
10M.2.Trinity.fasta 10M.5.Trinity.fasta 10M.10.Trinity.fasta 10M.20.Trinity.fasta raw.10M.Trinity.fasta \
10M.2.Trinity.fasta.pslx 10M.5.Trinity.fasta.pslx 10M.10.Trinity.fasta.pslx 10M.20.Trinity.fasta.pslx raw.10M.Trinity.fasta.pslx \
10M.2.Trinity.fasta.pep 10M.5.Trinity.fasta.pep 10M.10.Trinity.fasta.pep 10M.20.Trinity.fasta.pep raw.10M.Trinity.fasta.pep \
10M.2.xprs 10M.5.xprs 10M.10.xprs 10M.20.xprs raw.10M.xprs: 10M.left.2.fq 10M.left.5.fq 10M.left.10.fq 10M.left.20.fq 10M.right.2.fq 10M.right.5.fq 10M.right.10.fq 10M.right.20.fq
for TRIM in 20 2 5 10 0; do \
$(TRINITY)/Trinity.pl --full_cleanup --min_kmer_cov 1 --seqType fq --JM $(MEM)G --bflyHeapSpaceMax $(MEM)G \
--left 10M.left.$$TRIM.fq --right 10M.right.$$TRIM.fq --group_pairs_distance 999 --CPU $(CPU) --output 10M.$$TRIM; \
##FL Reconstruction
$(TRINITY)/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl --target $(MUS) --query 10M.$$TRIM.Trinity.fasta; rm *maps *selected *summary; \
##ORF ID
$(TRINITY)/trinity-plugins/transdecoder/transcripts_to_best_scoring_ORFs.pl --CPU $(CPU) -t 10M.$$TRIM.Trinity.fasta \
--search_pfam $(PFAM); \
rm longest_orfs* *gff3 *dat *scores *cds *bed *inx; mv best_candidates.eclipsed_orfs_removed.pep 10M.$$TRIM.Trinity.fasta.pep; \
<<<<<<< HEAD
bowtie2-build -q 10M.$$TRIM.Trinity.fasta index; echo -e '\n' Mapping at PHRED=$$trim '\n' >> 10M.$$TRIM.mapping.log; \
bowtie2 -p 12 -X 999 -k 30 -x index -1 $(READ1) -2 $(READ2) 2>>10M.$$TRIM.mapping.log | express -o 10.$$TRIM.xprs -p8 10M.$$TRIM.Trinity.fasta ; rm index* ; done
=======
##Mapping and eXpress
bowtie2-build -q 10M.$$TRIM.Trinity.fasta index; \
bowtie2 -p 12 -X 999 -k 30 -x index -1 $(READ1) -2 $(READ2) | express -o 10.$$TRIM.xprs -p8 10M.$$TRIM.Trinity.fasta >>10M.$$TRIM.mapping.log ; rm index* ; done
>>>>>>> a147beb60c68e837a1c79fb6213480f746e753fa
raw.20M.$(READ1) raw.20M.$(READ2):
python ~/error_correction/scripts/subsampler.py 20000000 $(READ1) $(READ2)
mv subsamp_1.fastq raw.20M.$(READ1)
mv subsamp_2.fastq raw.20M.$(READ2)
20M.left.2.fq 20M.left.5.fq 20M.left.10.fq 20M.left.20.fq 20M.right.2.fq 20M.right.5.fq 20M.right.10.fq 20M.right.20.fq:
@echo About to start trimming
for TRIM in 2 5 10 20 0; do \
java -Xmx$(MEM)g -jar $(TRIMMOMATIC) PE \
-phred33 -threads $(CPU) \
raw.20M.$(READ1) \
raw.20M.$(READ2) \
20M.$$TRIM.pp.1.fq \
20M.$$TRIM.up.1.fq \
20M.$$TRIM.pp.2.fq \
20M.$$TRIM.up.2.fq \
ILLUMINACLIP:$(BCODES):2:40:15 \
LEADING:$$TRIM \
TRAILING:$$TRIM \
SLIDINGWINDOW:4:$$TRIM \
MINLEN:25 1>> trim10.log; \
cat 20M.$$TRIM.pp.1.fq 20M.$$TRIM.up.1.fq > 20M.left.$$TRIM.fq ; \
cat 20M.$$TRIM.pp.2.fq 20M.$$TRIM.up.2.fq > 20M.right.$$TRIM.fq ; \
rm 20M.$$TRIM.pp.2.fq 20M.$$TRIM.up.2.fq 20M.$$TRIM.pp.1.fq 20M.$$TRIM.up.1.fq ; done
20M.2.Trinity.fasta 20M.5.Trinity.fasta 20M.10.Trinity.fasta 20M.20.Trinity.fasta raw.20M.Trinity.fasta \
20M.2.Trinity.fasta.pslx 20M.5.Trinity.fasta.pslx 20M.10.Trinity.fasta.pslx 20M.20.Trinity.fasta.pslx raw.20M.Trinity.fasta.pslx \
20M.2.Trinity.fasta.pep 20M.5.Trinity.fasta.pep 20M.10.Trinity.fasta.pep 20M.20.Trinity.fasta.pep raw.20M.Trinity.fasta.pep \
20M.2.xprs 20M.5.xprs 20M.10.xprs 20M.20.xprs raw.20M.xprs: 20M.left.2.fq 20M.left.5.fq 20M.left.10.fq 20M.left.20.fq 20M.right.2.fq 20M.right.5.fq 20M.right.10.fq 20M.right.20.fq
for TRIM in 20 2 5 10 0; do \
$(TRINITY)/Trinity.pl --full_cleanup --min_kmer_cov 1 --seqType fq --JM $(MEM)G --bflyHeapSpaceMax $(MEM)G \
--left 20M.left.$$TRIM.fq --right 20M.right.$$TRIM.fq --group_pairs_distance 999 --CPU $(CPU) --output 20M.$$TRIM; \
##FL Reconstruction
$(TRINITY)/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl --target $(MUS) --query 20M.$$TRIM.Trinity.fasta; rm *maps *selected *summary; \
##ORF ID
$(TRINITY)/trinity-plugins/transdecoder/transcripts_to_best_scoring_ORFs.pl --CPU $(CPU) -t 20M.$$TRIM.Trinity.fasta \
--search_pfam $(PFAM); \
rm longest_orfs* *gff3 *dat *scores *cds *bed *inx; mv best_candidates.eclipsed_orfs_removed.pep 20M.$$TRIM.Trinity.fasta.pep; \
<<<<<<< HEAD
bowtie2-build -q 20M.$$TRIM.Trinity.fasta index; echo -e '\n' Mapping at PHRED=$$trim '\n' >> 20M.$$TRIM.mapping.log; \
bowtie2 -p 12 -X 999 -k 30 -x index -1 $(READ1) -2 $(READ2) 2>>20M.$$TRIM.mapping.log | express -o 20.$$TRIM.xprs -p8 20M.$$TRIM.Trinity.fasta ; rm index* ; done
=======
##Mapping and eXpress
bowtie2-build -q 20M.$$TRIM.Trinity.fasta index; \
bowtie2 -p 12 -X 999 -k 30 -x index -1 $(READ1) -2 $(READ2) | express -o 10.$$TRIM.xprs -p8 20M.$$TRIM.Trinity.fasta >>20M.$$TRIM.mapping.log ; rm index* ; done
>>>>>>> a147beb60c68e837a1c79fb6213480f746e753fa
raw.50M.$(READ1) raw.50M.$(READ2):
python ~/error_correction/scripts/subsampler.py 50000000 $(READ1) $(READ2)
mv subsamp_1.fastq raw.50M.$(READ1)
mv subsamp_2.fastq raw.50M.$(READ2)
50M.left.2.fq 50M.left.5.fq 50M.left.10.fq 50M.left.20.fq 50M.right.2.fq 50M.right.5.fq 50M.right.10.fq 50M.right.20.fq:
@echo About to start trimming
for TRIM in 2 5 10 20 0; do \
java -Xmx$(MEM)g -jar $(TRIMMOMATIC) PE \
-phred33 -threads $(CPU) \
raw.50M.$(READ1) \
raw.50M.$(READ2) \
50M.$$TRIM.pp.1.fq \
50M.$$TRIM.up.1.fq \
50M.$$TRIM.pp.2.fq \
50M.$$TRIM.up.2.fq \
ILLUMINACLIP:$(BCODES):2:40:15 \
LEADING:$$TRIM \
TRAILING:$$TRIM \
SLIDINGWINDOW:4:$$TRIM \
MINLEN:25 1>> trim10.log; \
cat 50M.$$TRIM.pp.1.fq 50M.$$TRIM.up.1.fq > 50M.left.$$TRIM.fq ; \
cat 50M.$$TRIM.pp.2.fq 50M.$$TRIM.up.2.fq > 50M.right.$$TRIM.fq ; \
rm 50M.$$TRIM.pp.2.fq 50M.$$TRIM.up.2.fq 50M.$$TRIM.pp.1.fq 50M.$$TRIM.up.1.fq ; done
50M.2.Trinity.fasta 50M.5.Trinity.fasta 50M.10.Trinity.fasta 50M.20.Trinity.fasta raw.50M.Trinity.fasta \
50M.2.Trinity.fasta.pslx 50M.5.Trinity.fasta.pslx 50M.10.Trinity.fasta.pslx 50M.20.Trinity.fasta.pslx raw.50M.Trinity.fasta.pslx \
50M.2.Trinity.fasta.pep 50M.5.Trinity.fasta.pep 50M.10.Trinity.fasta.pep 50M.20.Trinity.fasta.pep raw.50M.Trinity.fasta.pep \
50M.2.xprs 50M.5.xprs 50M.10.xprs 50M.20.xprs raw.50M.xprs: 50M.left.2.fq 50M.left.5.fq 50M.left.10.fq 50M.left.20.fq 50M.right.2.fq 50M.right.5.fq 50M.right.10.fq 50M.right.20.fq
for TRIM in 20 2 5 10 0; do \
$(TRINITY)/Trinity.pl --full_cleanup --min_kmer_cov 1 --seqType fq --JM $(MEM)G --bflyHeapSpaceMax $(MEM)G \
--left 50M.left.$$TRIM.fq --right 50M.right.$$TRIM.fq --group_pairs_distance 999 --CPU $(CPU) --output 50M.$$TRIM; \
##FL Reconstruction
$(TRINITY)/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl --target $(MUS) --query 50M.$$TRIM.Trinity.fasta; rm *maps *selected *summary; \
##ORF ID
$(TRINITY)/trinity-plugins/transdecoder/transcripts_to_best_scoring_ORFs.pl --CPU $(CPU) -t 50M.$$TRIM.Trinity.fasta \
--search_pfam $(PFAM); \
rm longest_orfs* *gff3 *dat *scores *cds *bed *inx; mv best_candidates.eclipsed_orfs_removed.pep 50M.$$TRIM.Trinity.fasta.pep; \
<<<<<<< HEAD
bowtie2-build -q 50M.$$TRIM.Trinity.fasta index; echo -e '\n' Mapping at PHRED=$$trim '\n' >> 50M.$$TRIM.mapping.log; \
bowtie2 -p 12 -X 999 -k 30 -x index -1 $(READ1) -2 $(READ2) 2>>50M.$$TRIM.mapping.log | express -o 50.$$TRIM.xprs -p8 50M.$$TRIM.Trinity.fasta ; rm index* ; done
=======
##Mapping and eXpress
bowtie2-build -q 50M.$$TRIM.Trinity.fasta index; \
bowtie2 -p 12 -X 999 -k 30 -x index -1 $(READ1) -2 $(READ2) | express -o 10.$$TRIM.xprs -p8 50M.$$TRIM.Trinity.fasta >>50M.$$TRIM.mapping.log ; rm index* ; done
>>>>>>> a147beb60c68e837a1c79fb6213480f746e753fa
raw.75M.$(READ1) raw.75M.$(READ2):
python ~/error_correction/scripts/subsampler.py 75000000 $(READ1) $(READ2)
mv subsamp_1.fastq raw.75M.$(READ1)
mv subsamp_2.fastq raw.75M.$(READ2)
75M.left.2.fq 75M.left.5.fq 75M.left.10.fq 75M.left.20.fq 75M.right.2.fq 75M.right.5.fq 75M.right.10.fq 75M.right.20.fq:
@echo About to start trimming
for TRIM in 2 5 10 20 0; do \
java -Xmx$(MEM)g -jar $(TRIMMOMATIC) PE \
-phred33 -threads $(CPU) \
raw.75M.$(READ1) \
raw.75M.$(READ2) \
75M.$$TRIM.pp.1.fq \
75M.$$TRIM.up.1.fq \
75M.$$TRIM.pp.2.fq \
75M.$$TRIM.up.2.fq \
ILLUMINACLIP:$(BCODES):2:40:15 \
LEADING:$$TRIM \
TRAILING:$$TRIM \
SLIDINGWINDOW:4:$$TRIM \
MINLEN:25 1>> trim10.log; \
cat 75M.$$TRIM.pp.1.fq 75M.$$TRIM.up.1.fq > 75M.left.$$TRIM.fq ; \
cat 75M.$$TRIM.pp.2.fq 75M.$$TRIM.up.2.fq > 75M.right.$$TRIM.fq ; \
rm 75M.$$TRIM.pp.2.fq 75M.$$TRIM.up.2.fq 75M.$$TRIM.pp.1.fq 75M.$$TRIM.up.1.fq ; done
75M.2.Trinity.fasta 75M.5.Trinity.fasta 75M.10.Trinity.fasta 75M.20.Trinity.fasta raw.75M.Trinity.fasta \
75M.2.Trinity.fasta.pslx 75M.5.Trinity.fasta.pslx 75M.10.Trinity.fasta.pslx 75M.20.Trinity.fasta.pslx raw.75M.Trinity.fasta.pslx \
75M.2.Trinity.fasta.pep 75M.5.Trinity.fasta.pep 75M.10.Trinity.fasta.pep 75M.20.Trinity.fasta.pep raw.75M.Trinity.fasta.pep \
75M.2.xprs 75M.5.xprs 75M.10.xprs 75M.20.xprs raw.75M.xprs: 75M.left.2.fq 75M.left.5.fq 75M.left.10.fq 75M.left.20.fq 75M.right.2.fq 75M.right.5.fq 75M.right.10.fq 75M.right.20.fq
for TRIM in 20 2 5 10 0; do \
$(TRINITY)/Trinity.pl --full_cleanup --min_kmer_cov 1 --seqType fq --JM $(MEM)G --bflyHeapSpaceMax $(MEM)G \
--left 75M.left.$$TRIM.fq --right 75M.right.$$TRIM.fq --group_pairs_distance 999 --CPU $(CPU) --output 75M.$$TRIM; \
##FL Reconstruction
$(TRINITY)/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl --target $(MUS) --query 75M.$$TRIM.Trinity.fasta; rm *maps *selected *summary; \
##ORF ID
$(TRINITY)/trinity-plugins/transdecoder/transcripts_to_best_scoring_ORFs.pl --CPU $(CPU) -t 75M.$$TRIM.Trinity.fasta \
--search_pfam $(PFAM); \
rm longest_orfs* *gff3 *dat *scores *cds *bed *inx; mv best_candidates.eclipsed_orfs_removed.pep 75M.$$TRIM.Trinity.fasta.pep; \
<<<<<<< HEAD
bowtie2-build -q 75M.$$TRIM.Trinity.fasta index; echo -e '\n' Mapping at PHRED=$$trim '\n' >> 75M.$$TRIM.mapping.log; \
bowtie2 -p 12 -X 999 -k 30 -x index -1 $(READ1) -2 $(READ2) 2>>75M.$$TRIM.mapping.log | express -o 75.$$TRIM.xprs -p8 75M.$$TRIM.Trinity.fasta ; rm index* ; done
=======
##Mapping and eXpress
bowtie2-build -q 75M.$$TRIM.Trinity.fasta index; \
bowtie2 -p 12 -X 999 -k 30 -x index -1 $(READ1) -2 $(READ2) | express -o 10.$$TRIM.xprs -p8 75M.$$TRIM.Trinity.fasta >>75M.$$TRIM.mapping.log ; rm index* ; done
>>>>>>> a147beb60c68e837a1c79fb6213480f746e753fa
raw.100M.$(READ1) raw.100M.$(READ2):
python ~/error_correction/scripts/subsampler.py 100000000 $(READ1) $(READ2)
mv subsamp_1.fastq raw.100M.$(READ1)
mv subsamp_2.fastq raw.100M.$(READ2)
100M.left.2.fq 100M.left.5.fq 100M.left.10.fq 100M.left.20.fq 100M.right.2.fq 100M.right.5.fq 100M.right.10.fq 100M.right.20.fq:
@echo About to start trimming
for TRIM in 2 5 10 20 0; do \
java -Xmx$(MEM)g -jar $(TRIMMOMATIC) PE \
-phred33 -threads $(CPU) \
raw.100M.$(READ1) \
raw.100M.$(READ2) \
100M.$$TRIM.pp.1.fq \
100M.$$TRIM.up.1.fq \
100M.$$TRIM.pp.2.fq \
100M.$$TRIM.up.2.fq \
ILLUMINACLIP:$(BCODES):2:40:15 \
LEADING:$$TRIM \
TRAILING:$$TRIM \
SLIDINGWINDOW:4:$$TRIM \
MINLEN:25 1>> trim10.log; \
cat 100M.$$TRIM.pp.1.fq 100M.$$TRIM.up.1.fq > 100M.left.$$TRIM.fq ; \
cat 100M.$$TRIM.pp.2.fq 100M.$$TRIM.up.2.fq > 100M.right.$$TRIM.fq ; \
rm 100M.$$TRIM.pp.2.fq 100M.$$TRIM.up.2.fq 100M.$$TRIM.pp.1.fq 100M.$$TRIM.up.1.fq ; done
100M.2.Trinity.fasta 100M.5.Trinity.fasta 100M.10.Trinity.fasta 100M.20.Trinity.fasta raw.100M.Trinity.fasta \
100M.2.Trinity.fasta.pslx 100M.5.Trinity.fasta.pslx 100M.10.Trinity.fasta.pslx 100M.20.Trinity.fasta.pslx raw.100M.Trinity.fasta.pslx \
100M.2.Trinity.fasta.pep 100M.5.Trinity.fasta.pep 100M.10.Trinity.fasta.pep 100M.20.Trinity.fasta.pep raw.100M.Trinity.fasta.pep \
100M.2.xprs 100M.5.xprs 100M.10.xprs 100M.20.xprs raw.100M.xprs: 100M.left.2.fq 100M.left.5.fq 100M.left.10.fq 100M.left.20.fq 100M.right.2.fq 100M.right.5.fq 100M.right.10.fq 100M.right.20.fq
for TRIM in 20 2 5 10 0; do \
$(TRINITY)/Trinity.pl --full_cleanup --min_kmer_cov 1 --seqType fq --JM $(MEM)G --bflyHeapSpaceMax $(MEM)G \
--left 100M.left.$$TRIM.fq --right 100M.right.$$TRIM.fq --group_pairs_distance 999 --CPU $(CPU) --output 100M.$$TRIM; \
##FL Reconstruction
$(TRINITY)/Analysis/FL_reconstruction_analysis/FL_trans_analysis_pipeline.pl --target $(MUS) --query 100M.$$TRIM.Trinity.fasta; rm *maps *selected *summary; \
##ORF ID
$(TRINITY)/trinity-plugins/transdecoder/transcripts_to_best_scoring_ORFs.pl --CPU $(CPU) -t 100M.$$TRIM.Trinity.fasta \
--search_pfam $(PFAM); \
rm longest_orfs* *gff3 *dat *scores *cds *bed *inx; mv best_candidates.eclipsed_orfs_removed.pep 100M.$$TRIM.Trinity.fasta.pep; \
<<<<<<< HEAD
bowtie2-build -q 100M.$$TRIM.Trinity.fasta index; echo -e '\n' Mapping at PHRED=$$trim '\n' >> 100M.$$TRIM.mapping.log; \
bowtie2 -p 12 -X 999 -k 30 -x index -1 $(READ1) -2 $(READ2) 2>>100M.$$TRIM.mapping.log | express -o 100.$$TRIM.xprs -p8 100M.$$TRIM.Trinity.fasta ; rm index* ; done
=======
##Mapping and eXpress
bowtie2-build -q 100M.$$TRIM.Trinity.fasta index; \
bowtie2 -p 12 -X 999 -k 30 -x index -1 $(READ1) -2 $(READ2) | express -o 10.$$TRIM.xprs -p8 100M.$$TRIM.Trinity.fasta >>100M.$$TRIM.mapping.log ; rm index* ; done
>>>>>>> a147beb60c68e837a1c79fb6213480f746e753fa