Pipeline steps
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Quality statistics (fastq level) -
fastqc -
htseq-qa -
fastp (fastqc, htseq-qa)
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Remove adapters (5', 3' polyA tail) -
cutadapt -
fastp
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Create index for mapping -
STAR
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Map reads -
STAR -
add feature two-pass mode -
multimappers -
End to End
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Quality statistics (bam level) -
Estimate gene/transcript expression -
salmon on fastq file -
kallisto on fastq file
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Summary -
Create gene expression table of -
TPM -
Normalized (raw) reads -
multiqc
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Edited by Alex Kanitz