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annotate test-data/test_data_generation.sh @ 0:7d8cafa4d18c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
author iuc
date Sat, 13 May 2023 12:31:25 +0000
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7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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1 cd /home/ldelisle/Documents/mygit/tools-iuc/tools/rgrnastar/test-data
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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2 STAR --runMode genomeGenerate --genomeDir 'tempstargenomedir' --genomeFastaFiles filtered3.Homo_sapiens.GRCh38.dna.chromosome.21.fa --sjdbOverhang 100 --sjdbGTFfile filtered3.Homo_sapiens.GRCh38.100.chr21.gtf --genomeSAindexNbases 4
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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3 STAR --genomeLoad NoSharedMemory --genomeDir tempstargenomedir --soloType CB_UMI_Simple --readFilesIn pbmc_1k_v2_L001.R2.10k.fastq.gz pbmc_1k_v2_L001.R1.10k.fastq.gz --soloCBmatchWLtype 1MM_multi_pseudocounts --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloUMIlen 12 --soloCBwhitelist filtered.barcodes.txt --soloBarcodeReadLength 1 --readFilesCommand zcat --outSAMattributes NH AS HI nM CB UB --outSAMtype BAM SortedByCoordinate
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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4 mv Aligned.sortedByCoord.out.bam ../../velocyto/test-data/STARsolo_allSAMat.bam
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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5 mv Solo.out/Gene/filtered/barcodes.tsv ../../velocyto/test-data/
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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6
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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7 cd ../../velocyto/test-data/
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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8 mkdir -p sample/outs/filtered_gene_bc_matrices/whatever/
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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9 ln -s $PWD/barcodes.tsv sample/outs/filtered_gene_bc_matrices/whatever/
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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10 ln -s $PWD/STARsolo_allSAMat.bam sample/outs/possorted_genome_bam.bam
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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11 velocyto run10x sample ./filtered3.Homo_sapiens.GRCh38.100.chr21.gtf
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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12 rm -r sample/velocyto
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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13 velocyto run -c -U ./STARsolo_allSAMat.bam ./filtered3.Homo_sapiens.GRCh38.100.chr21.gtf
7d8cafa4d18c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/velocyto commit d9beec424754fdf4f0b125552115521f9f536cb8
iuc
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14 velocyto run -c -U ./STARsolo_allSAMat.bam ./STARsolo_allSAMat.bam ./filtered3.Homo_sapiens.GRCh38.100.chr21.gtf