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mikelove/minimap2_to_Salmon

Created September 21, 2023 11:45
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minimap2 -> Salmon
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minimap2_to_Salmon
# minimap2 map reads:
minimap2 -t {threads} -a -x map-ont -p 1.0 -N 100 {input.index} {input.fastq} | samtools view -Sb > {output.bam}
# salmon Quant:
salmon quant --ont --noLengthCorrection -p 8 -t {input.transcriptome} -l U -a {input.bam} -o {output}
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