09.RNASEQ_genome_level.md

RNA-Seq: genome-level

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Note

Perform RNA-Seq analysis using diploid genomes

salmon index -p 12 -t seq/${ref_name}.gentrome.fasta -i salmon/${ref_name}_k31 -k 31 -d seq/${ref_name}.decoys.txt > salmon/${ref_name}_k31.log 2> salmon/${ref_name}_k31.err

salmon quant -p 24 -i salmon/${ref_name} -l A -1 ${read1} -2 ${read2} --seqBias --gcBias --validateMappings -o salmon/counts/${name}.on.${ref_name}_quant > salmon/${name}.on.${ref_name}_quant.log 2> salmon/${name}.on.${ref_name}_quant.err

optimize dma <- Previous Step | home | Next Step -> allelic pairs