length_plot(obj0) 错误: 找不到对象'sample_group'

[liuqi6786]

gp <- c("Col0_MOCK_1","Col0_MOCK_2","Col0_MOCK_3",
"tmk14_MOCK_1","tmk14_MOCK_2","tmk14_MOCK_3")

ribobams <- c("Ribo_Col0_MOCK_1.bam","Ribo_Col0_MOCK_2.bam","Ribo_Col0_MOCK_3.bam",
"Ribo_tmk14_MOCK_1.bam","Ribo_tmk14_MOCK_2.bam","Ribo_tmk14_MOCK_3.bam")

构建 ribotrans object

obj0 <- construct_ribotrans(
genome_file = "Arabidopsis_thaliana.TAIR10.dna.toplevel.fa",
gtf_file = "Arabidopsis_thaliana.TAIR10.60.gtf",
mapping_type = "genome", # 或 "transcriptome"
assignment_mode = "end5",
extend = TRUE,
extend_upstream = 50,
extend_downstream = 50,
Ribo_bam_file = ribobams,
Ribo_sample_name = gp,
choose_longest_trans = TRUE
) 这是我的代码，输出的obj0和您网页的也是一样的，但是后续的分析就是进行不下去了

[junjunlab]

你可以加我微信

[junjunlab]

QC前需要先运行generate_summary,详情见https://junjunlab.github.io/riboTransVis-manual/Quality-assessment.html：

# generate summary data for QC or other analysis
obj0 <- generate_summary(object = obj0, exp_type = "ribo", nThreads = 20)