ribotish and umi_tools merge request

src/FLOSS_score/Makefile-align-mesc

+SHELL=/bin/bash -x
+
+all:
+
+.SECONDARY:
+
+include samples.d
+
+NEW_SAMPLES=ribo_chx_mesc ribo_emet_mesc
+OLD_SAMPLES=ribo_chx_oldmesc ribo_emet_oldmesc ribo_harr120_oldmesc ribo_harr150_oldmesc
+RIBO_SAMPLES=$(NEW_SAMPLES) $(OLD_SAMPLES)
+SAMPLES=$(RIBO_SAMPLES)
+PROJECTS=/mnt/ingolialab/FastQ/121204_SN375_0200_AC1A7LACXX/FastQ/Project_NI-nickingolia-ESdrug/ \
+	/mnt/ingolialab/FastQ/130305_SN375_0214_AC1CACACXX/FastQ/Project_NI-nickingolia/ \
+	/mnt/ingolialab/FastQ/130709_SN375_0236_BD294UACXX/FastQ-i4n3/Project_NI-nickingolia/
+
+ribo_emet_oldmesc_trim.fq:  /mnt/ingolialab/ingolia/MouseES/RawData/100426/s_3_sequence.txt.bz2
+ribo_chx_oldmesc_trim.fq: /mnt/ingolialab/ingolia/MouseES/RawData/100426/s_5_sequence.txt.bz2
+ribo_chx_oldmesc_trim.fq: /mnt/ingolialab/ingolia/MouseES/RawData/100809/s_4_sequence.txt.bz2
+ribo_harr120_oldmesc_trim.fq: /mnt/ingolialab/ingolia/MouseES/RawData/100706/s_5_sequence.txt.bz2
+ribo_harr120_oldmesc_trim.fq: /mnt/ingolialab/ingolia/MouseES/RawData/100706/s_6_sequence.txt.bz2
+ribo_harr150_oldmesc_trim.fq: /mnt/ingolialab/ingolia/MouseES/RawData/100624/s_2_sequence.txt.bz2
+ribo_harr150_oldmesc_trim.fq: /mnt/ingolialab/ingolia/MouseES/RawData/100706/s_2_sequence.txt.bz2
+
+# RUNTIME CONFIGURATION
+BOWTIE_PARALLEL=-p 32
+TOPHAT_KEEP_TEMP=#--keep-tmp
+
+# LINKER TRIMMING CONFIGURATION
+NI_NI_9=CTGTAGGCACCATCAATAGA
+
+FP_LINKER=$(NI_NI_9)
+FP_MIN_INSERT=24
+
+# RRNA ALIGNMENT CONFIGURATION
+RRNA_MAQ_ERR=60
+RRNA_SEEDLEN=23
+RRNA_MAXREAD=51
+
+RRNA_EBWT=/mnt/ingolialab/ingolia/Genomes/SpikeIn/mm-scspike-rrna
+
+# GENOME ALIGNMENT CONFIGURATION
+TOPHAT_EBWT=/mnt/ingolialab/ingolia/Genomes/SpikeIn/mm10-scspike
+TOPHAT_GTF=Mm.GRCm38.72-plus-scspike.gtf
+
+# BINARIES
+TOPHAT=tophat
+BOWTIE=bowtie
+SAMTOOLS=samtools
+TAM_TO_BAM=$(SAMTOOLS) view -b -S -h -
+
+# Fix up chromosome names for Ensembl
+Mm.GRCm38.72.gtf: Mus_musculus.GRCm38.72.gtf
+	awk -F$$'\t' '/^[0-9XY]/ { printf("chr%s\n", $$0) } /^MT/ { gsub(/^MT/, "chrM", $$0); print }' $< > $@
+
+$(TOPHAT_GTF): Mm.GRCm38.72.gtf /mnt/ingolialab/ingolia/Genomes/SpikeIn/sac_cer_spike.gtf
+	cat $^ > $@
+
+samples.d: $(PROJECTS)
+	ls $(addsuffix /Sample_*/*.fastq.gz,$(PROJECTS)) | \
+	  sed 's,.*Sample_\(.*\)/.*\.fastq\.gz$$,\1_trim.fq: &,' | \
+	  sed s/ribo_mesc_chx/ribo_chx_mesc/ | \
+	  sed s/ribo_mesc_emet/ribo_emet_mesc/ \
+	  > $@
+
+trims:   $(addsuffix _trim.fq, $(SAMPLES))
+norrnas: $(addsuffix _norrna.fq, $(SAMPLES))
+genomic: $(addsuffix _genome_sorted.bam.bai, $(SAMPLES))
+
+all: trims
+all: norrnas
+all: genomic
+
+# RIBO LINKER TRIMMING
+$(addsuffix _trim.fq, $(NEW_SAMPLES)): %_trim.fq:
+	mkdir -p Statistics
+	zcat $^ \
+	  | fastx_clipper -Q33 -a $(FP_LINKER) -l $(FP_MIN_INSERT) -c -n -v 2>Statistics/$*_clip.txt \
+	  > $@
+
+$(addsuffix _trim.fq, $(OLD_SAMPLES)): %_trim.fq:
+	mkdir -p Statistics
+	bzcat $^ \
+	  | fastx_clipper -Q33 -a $(FP_LINKER) -l $(FP_MIN_INSERT) -c -n -v 2>Statistics/$*_clip.txt \
+	  > $@
+
+# RRNA ALIGNMENTS
+RRNA_BOWTIE_ARGS=$(BOWTIE_PARALLEL) --solexa-quals --maqerr=$(RRNA_MAQ_ERR) --seedlen=$(RRNA_SEEDLEN)
+
+$(addsuffix _norrna.fq, $(RIBO_SAMPLES)):%_norrna.fq: %_trim.fq
+	mkdir -p Statistics
+	bowtie $(RRNA_BOWTIE_ARGS) --un $@ --sam $(RRNA_EBWT) $< 2>Statistics/$*_rrna.txt > /dev/null
+
+# GENOME ALIGNMENTS
+TOPHAT_ARGS=$(BOWTIE_PARALLEL) --solexa-quals --GTF $(TOPHAT_GTF) --no-novel-juncs --library-type fr-unstranded $(TOPHAT_KEEP_TEMP)
+
+$(addsuffix _genome/accepted_hits.bam, $(SAMPLES)): %_genome/accepted_hits.bam: %_norrna.fq $(TOPHAT_EBWT).1.ebwt $(TOPHAT_GTF)
+	mkdir -p Statistics
+	$(TOPHAT) $(TOPHAT_ARGS) --output-dir $(dir $@) $(TOPHAT_EBWT) $< 2>Statistics/$*_genome.txt
+
+%_sorted.bam.bai: %_sorted.bam
+	$(SAMTOOLS) index $< 2>Statistics/$*_genome_index.txt
+
+$(addsuffix _genome_sorted.bam, $(SAMPLES)): %_genome_sorted.bam: %_genome/accepted_hits.bam
+	samtools view -h $^ | \
+	  grep -E '(NM:i:[01])|(^@)' | \
+	  samtools view -S -b - > $@
+