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all: paired single samples_file
test: all
paired:
${TRINITY_HOME}/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py \
--st_fa supertranscripts.fasta \
--st_gtf supertranscripts.gtf \
-p whitefly_rnaseq_1.fq.gz whitefly_rnaseq_2.fq.gz \
-o test_varcalling_paired \
--rg_id whitefly_id --rg_sample whitefly_sample
test: all
single:
${TRINITY_HOME}/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py \
--st_fa supertranscripts.fasta \
--st_gtf supertranscripts.gtf \
-s whitefly_rnaseq_1.fq.gz \
-o test_varcalling_single \
--rg_id whitefly_id --rg_sample whitefly_sample
samples_file:
${TRINITY_HOME}/Analysis/SuperTranscripts/AllelicVariants/run_variant_calling.py \
--st_fa supertranscripts.fasta \
--st_gtf supertranscripts.gtf \
-S samples_file.txt \
-o test_varcalling_samplesfile
clean:
rm -f ./*.log ./*.dict ./*.fai
rm -rf ./test_varcalling_paired ./test_varcalling_single ./test_varcalling_samplesfile
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