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command_lines.txt
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command_lines.txt
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AlevinIndexFB:
salmon index --no-version-check -t hto.tsv -i idx_fb --features -k7
awk 'OFS= {print $1, $1}' hto.tsv > idx_fb/tgmap.txt
AlevinQC:sample1
Rscript --vanilla /home/runner/work/sc_preprocess/sc_preprocess/bin/alevin_qc.R sample1 sample1
AlevinQC:sample1_fb
Rscript --vanilla /home/runner/work/sc_preprocess/sc_preprocess/bin/alevin_qc.R sample1_fb sample1_fb
AlevinQC:sample2
Rscript --vanilla /home/runner/work/sc_preprocess/sc_preprocess/bin/alevin_qc.R sample2 sample2
AlevinQC:sample3
Rscript --vanilla /home/runner/work/sc_preprocess/sc_preprocess/bin/alevin_qc.R sample3 sample3
AlevinQC:sample3_fb
Rscript --vanilla /home/runner/work/sc_preprocess/sc_preprocess/bin/alevin_qc.R sample3_fb sample3_fb
INDEXING:AlevinIndex:
gzip -cd example_genome.fa.gz | grep '^>' | cut -d -f 1 | awk '{gsub(>,);print}' > decoynames.txt
cat annotation.expanded.fa.gz example_genome.fa.gz > gentrome.fa.gz
salmon index --no-version-check -t gentrome.fa.gz -d decoynames.txt -i idx_gentrome -p 1 --sparse
INDEXING:ParseExonIntronTx:
Rscript --vanilla /home/runner/work/sc_preprocess/sc_preprocess/bin/parse_introns.R example_genome.fa.gz example_annot.gtf.gz gene_id gene_name gene_type 150 chrM Mt_rRNA
Mtx:sample1
Rscript --vanilla /home/runner/work/sc_preprocess/sc_preprocess/bin/mtx.R --sampleid sample1 --alevin_rna sample1 --alevin_fb sample1_fb --expanded_features annotation.expanded.features.tsv.gz --gene2type annotation.gene2type.txt --translate_table translate_list.txt.gz --do_translate
Mtx:sample2
Rscript --vanilla /home/runner/work/sc_preprocess/sc_preprocess/bin/mtx.R --sampleid sample2 --alevin_rna sample2 --expanded_features annotation.expanded.features.tsv.gz --gene2type annotation.gene2type.txt
Mtx:sample3
Rscript --vanilla /home/runner/work/sc_preprocess/sc_preprocess/bin/mtx.R --sampleid sample3 --alevin_rna sample3 --alevin_fb sample3_fb --expanded_features annotation.expanded.features.tsv.gz --gene2type annotation.gene2type.txt --translate_table translate_list.txt.gz --do_translate
Quant:sample1
salmon alevin --no-version-check -i idx_gentrome --tgMap annotation.expanded.tx2gene.tsv --mrna annotation.mtRNA.txt --rrna annotation.rRNA.txt -o sample1 -l ISR -p 1 --dumpFeatures --bc-geometry 1[1-16] --umi-geometry 1[17-28] --read-geometry 2[1-91] --forceCells 1000 -1 sample1_1.fastq.gz sample1a_1.fastq.gz -2 sample1_2.fastq.gz sample1a_2.fastq.gz
Quant:sample2
salmon alevin --no-version-check -i idx_gentrome --tgMap annotation.expanded.tx2gene.tsv --mrna annotation.mtRNA.txt --rrna annotation.rRNA.txt -o sample2 -l ISR -p 1 --dumpFeatures --bc-geometry 1[1-16] --umi-geometry 1[17-28] --read-geometry 2[1-91] --forceCells 1000 -1 sample2_1.fastq.gz -2 sample2_2.fastq.gz
Quant:sample3
salmon alevin --no-version-check -i idx_gentrome --tgMap annotation.expanded.tx2gene.tsv --mrna annotation.mtRNA.txt --rrna annotation.rRNA.txt -o sample3 -l ISR -p 1 --dumpFeatures --bc-geometry 1[1-16] --umi-geometry 1[17-28] --read-geometry 2[1-91] --forceCells 1000 -1 sample3_1.fastq.gz -2 sample3_2.fastq.gz
QuantFB:sample1
salmon alevin --no-version-check -i idx_fb --tgMap tgmap.txt -o sample1_fb -l ISR -p 1 --dumpFeatures --keepCBFraction 1.0 --bc-geometry 1[1-16] --umi-geometry 1[17-28] --read-geometry 2[11-25] --forceCells 1000 -1 sample1SF_1.fastq.gz -2 sample1SF_2.fastq.gz
QuantFB:sample3
salmon alevin --no-version-check -i idx_fb --tgMap tgmap.txt -o sample3_fb -l ISR -p 1 --dumpFeatures --keepCBFraction 1.0 --bc-geometry 1[1-16] --umi-geometry 1[17-28] --read-geometry 2[11-25] --forceCells 1000 -1 sample3SF_1.fastq.gz -2 sample3SF_2.fastq.gz
VALIDATE:ValidateSamplesheet:
Rscript --vanilla /home/runner/work/sc_preprocess/sc_preprocess/bin/validate_samplesheet.R samplesheet.csv
WriteNcells:
Rscript --vanilla /home/runner/work/sc_preprocess/sc_preprocess/bin/summary.R