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$ python rnaQUAST.py --threads 4 --blat --transcripts test_data/idba.fasta test_data/spades.311.fasta test_data/Trinity.fasta --reference test_data/Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa --gene_database test_data/Saccharomyces_cerevisiae.R64-1-1.75.gtf --output_dir ~/rnaQUAST_test_output_blatBLAT |
Read alignment:
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rnaQUAST 1.1.0 is also capable of calculating various statistics using raw reads (e.g. database coverage by reads) using either STAR aligner (or alternatively TopHat aligner +SAM tools) |
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$ python rnaQUAST.py --threads 2 --transcripts test_data/idba.fasta test_data/spades.311.fasta test_data/Trinity.fasta --left_reads test_data/Paired_ends1.fq --right_reads test_data/Paired_ends2.fq --reference test_data/Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa --gene_database test_data/Saccharomyces_cerevisiae.R64-1-1.75.gtf --output_dir ~/rnaQUAST_test_outoutput_STAR |
b. Using rnaQUAST 1.1.0 tool using TopHat aligner +SAM tools
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$ python rnaQUAST.py --no_plots --threads 2 --transcripts test_data/idba.fasta test_data/spades.311.fasta test_data/Trinity.fasta --left_reads test_data/Paired_ends1.fq --right_reads test_data/Paired_ends2.fq --reference test_data/Saccharomyces_cerevisiae.R64-1-1.75.dna.toplevel.fa --gene_database test_data/Saccharomyces_cerevisiae.R64-1-1.75.gtf --output_dir ~/rnaQUAST_test_outoutput_tophatTOPHAT --tophat |
Software for de novo quality assessment:
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$ python rnaQUAST.py --threads 4 --transcripts test_data/idba.fasta test_data/spades.311.fasta test_data/Trinity.fasta --output_dir ~/rnaQUAST_test_outoutput_arthropoda_BUSCO --disable_infer_genes --disable_infer_transcripts --busco --clade /opt/rnaQUAST-1.1.0/BUSCO_v1.1b1/arthropoda |
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$ python rnaQUAST.py --threads 4 --transcripts test_data/idba.fasta test_data/spades.311.fasta test_data/Trinity.fasta --output_dir ~/rnaQUAST_test_outoutput_GM --gene_mark
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For detailed explanation of the outputs with each of the above runs, please refer to rnaQUAST 1.1.0 manual |
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