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run_salmon.sh
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#./tools/salmon-1.9.0/bin/salmon quant \
# -i nmr_index -l A \
# -1 ../../data/rnaseq/naked_mole_rat/SRR2123747_pass_1_trimmed.fastq.gz \
# -2 ../../data/rnaseq/naked_mole_rat/SRR2123747_pass_2_trimmed.fastq.gz \
# --threads 7 --validateMappings -o quants/SRR2123747_quant
#./tools/salmon-1.9.0/bin/salmon quant \
# -i bw_index -l A \
# -1 ../../data/rnaseq/bowhead_whale/SRR1685415_pass_1_trimmed.fastq.gz \
# -2 ../../data/rnaseq/bowhead_whale/SRR1685415_pass_2_trimmed.fastq.gz \
# --threads 7 --validateMappings -o quants/SRR1685415_quant
#./tools/salmon-1.9.0/bin/salmon quant \
# -i m_index -l A \
# -1 ../../data/rnaseq/mouse/SRR1302402_pass_1_trimmed.fastq.gz \
# -2 ../../data/rnaseq/mouse/SRR1302402_pass_2_trimmed.fastq.gz \
# --threads 7 --validateMappings -o quants/SRR1302402_quant
#./tools/salmon-1.9.0/bin/salmon quant \
# -i bb_index -l A \
# -1 ../../data/rnaseq/brandts_bat/SRR617087_pass_1_trimmed.fastq.gz \
# -2 ../../data/rnaseq/brandts_bat/SRR617087_pass_2_trimmed.fastq.gz \
# --threads 7 --validateMappings -o quants/SRR617087_quant
#./tools/salmon-1.9.0/bin/salmon quant \
# -i c_index -l A \
# -1 ../../data/rnaseq/cow/SRR594477_pass_1_trimmed.fastq.gz \
# -2 ../../data/rnaseq/cow/SRR594477_pass_2_trimmed.fastq.gz \
# --threads 7 --validateMappings -o quants/SRR594477_quant
./tools/salmon-1.9.0/bin/salmon quant \
-i gw_index -l A \
-1 ../../data/rnaseq/gray_whale/SRR13853443_pass_1_trimmed.fastq.gz \
-2 ../../data/rnaseq/gray_whale/SRR13853443_pass_2_trimmed.fastq.gz \
--threads 7 --validateMappings -o quants/SRR13853443_quant