导读

主页：http://hammelllab.labsites.cshl.edu/software/
Github：https://github.com/mhammell-laboratory/TEtranscripts
文献：TEtranscripts: a package for including transposable elements in differential expression analysis of RNA-seq datasets. Bioinformatics 2015
文献：https://academic.oup.com/bioinformatics/article/31/22/3593/240793#supplementary-data

TEtranscripts flow chart

一、conda安装TEtranscripts

conda install TEtranscripts
TEtranscripts -h

识别基因差异转录本和转座原件

二、下载curated GTF文件

三、TEtranscripts识别基因差异转录本和转座原件

基本用法[帮助文档]

TEtranscripts --mode multi \
-t RNAseq1.bam RNAseq2.bam \
-c control_RNAseq1.bam control_RNAseq2.bam \
--GTF gene_annotation.gtf \
--TE TE_annotation.gtf \
--project TEtranscripts_out
--sortByPos

If BAM files are unsorted, or sorted by queryname:

TEtranscripts --format BAM --mode multi \
-t RNAseq1.bam RNAseq2.bam \
-c CtlRNAseq1.bam CtlRNAseq.bam \
--project sample_nosort_test

If BAM files are sorted by coordinates/position:

TEtranscripts --format BAM --mode multi \
-t RNAseq1.bam RNAseq2.bam \
-c CtlRNAseq1.bam CtlRNAseq.bam \
--project sample_nosort_test \
--sortByPos

四、TEcount计算每个样品TE转座原件的表达

TEcount -h

TEcount --mode multi \
-b RNAseq.bam \
--GTF gene_annotation.gtf \
--TE TE_annotation.gtf \
--project sample_TEcount_out \
--sortByPos

If BAM files are unsorted, or sorted by queryname:

TEcount --format BAM --mode multi \
-b RNAseq.bam \
--project sample_nosort_test

If BAM files are sorted by coordinates/position:

TEtranscripts --format BAM --mode multi \
-b RNAseq.bam \
--project sample_sorted_test \
--sortByPos