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test:
${TRINITY_HOME}/Trinity --samples_file samples_n_reads_decribed.txt --seqType fq --SS_lib_type RF --max_memory 1G --trimmomatic
${TRINITY_HOME}/util/align_and_estimate_abundance.pl --transcripts trinity_out_dir/Trinity.fasta --est_method RSEM --aln_method bowtie2 --prep_reference --trinity_mode --samples_file samples_n_reads_decribed.txt --seqType fq
find . -maxdepth 2 -name "*RSEM.isoforms.results" | tee rsem.isoform.files
${TRINITY_HOME}/util/abundance_estimates_to_matrix.pl --est_method RSEM --name_sample_by_basedir --quant_files rsem.isoform.files --out_prefix rsem --gene_trans_map trinity_out_dir/Trinity.fasta.gene_trans_map
${TRINITY_HOME}/Analysis/DifferentialExpression/run_DE_analysis.pl -m rsem.isoform.counts.matrix -s samples_n_reads_decribed.txt --method edgeR -o edgeR_isoforms --dispersion 0.1
${TRINITY_HOME}/Analysis/DifferentialExpression/run_DE_analysis.pl -m rsem.gene.counts.matrix -s samples_n_reads_decribed.txt --method edgeR -o edgeR_genes --dispersion 0.1
${TRINITY_HOME}/util/misc/fasta_seq_length.pl trinity_out_dir/Trinity.fasta > Trinity.fasta.seq_lens
${TRINITY_HOME}/util/misc/TPM_weighted_gene_length.py --gene_trans_map trinity_out_dir/Trinity.fasta.gene_trans_map --trans_lengths Trinity.fasta.seq_lens --TPM_matrix rsem.isoform.TMM.EXPR.matrix > Trinity.gene_lengths.txt
touch test
clean:
./cleanme.pl
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