transcript abundance

extract gene-level expression measurements from ballgown objects

For objects created with Cufflinks/Tablemaker, gene-level measurements are calculated by appropriately combining FPKMs from the transcripts comprising the gene. For objects created with RSEM, gene-level measurements are extracted directly from the RSEM output.

Import transcript-level estimates

• Salmon (Patro et al. 2017)
• Alevin (Srivastava et al. 2019)
• Sailfish (Patro, Mount, and Kingsford 2014)
• kallisto (Bray et al. 2016)
• RSEM (Li and Dewey 2011)
• StringTie (Pertea et al. 2015)

https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html

1 转录本拼接

2 转录本表达定量1111

图片alt

基因组的3个exon可以转录出两个转录本t1和t2，可以从exon的表达量，推算出转录本的表达量

2.1 转本表达定量 VS 基因表达定量

参考

• Explore Transcriptome using NGS