TEtranscripts文章引用参数

GitHub - mhammell-laboratory/TEtranscripts: A package for including transposable elements in differential enrichment analysis of sequencing datasets.

官网里面的用法，推荐是STAR --outFilterMultimapNmax 100 -winAnchorMultimapNmax 100

1【LINE-1 retrotransposons drive human neuronal transcriptome complexity and functional diversification】Sci Adv. 2023 Nov 3

用star比对到hg38，参数为--outFilterMultimapNmax 100 -winAnchorMultimapNmax 200，然后再用TEcount的multi计数

2【Cellular RNA and DNA sensing pathways are essential for the dose-dependent response of human monocytes to ionizing radiation】

比对到hg38，用TEcount得到count，然后count标准化为cpm，用全部蛋白编码基因+TE，进行cpm标化

3【Chemical-induced phase transition and global conformational reorganization of chromatin】Nat Commun. 2023

比对到star上–winAnchorMultimapNmax 200 and --outFilterMultimapNmax 100

4【A fast chemical reprogramming system promotes cell identity transition through a diapause-like state】Nat Cell Biol. 2023 Aug

用参数-sortByPos-format BAM -mode multi，并且用CPM标化

5【Transient naive reprogramming corrects hiPS cells functionally and epigenetically】Nature. 2023

同时用了TEtranscripts和TElocal

6【Dot1l cooperates with Npm1 to repress endogenous retrovirus MERVL in embryonic stem cells】Nucleic Acids Res. 2023 Sep

同时用了TEtranscripts和TElocal