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- When mapping to the genome (using a tool like hisat2), use a tool (eg: bedtools, htseq,stringtie) to get gene/transcript counts from mapping results.
- Transcript counting is tricky: It involves assigning a read to a specific transcript of a gene and counting it towards that transcript.
- When mapping to the transcriptome using kallisto) you do not need to do an extra step of gene/transcript counting.
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