GSE145805 SHAPE-seq Data Processing
SHAPE-seq
geo_data_processing
7 steps
Publication
Evaluation of novel computational methods to identify RNA-binding protein footprints from structural data.RNA (New York, N.Y.) (2025) — PMID 40399037
Warning: Pipeline descriptions and code snippets may be inferred or AI-generated. Use them only as a starting point to guide analysis, and validate before use.
Processing Steps
Generate Jupyter Notebook-
1
Library strategy: icSHAPE
SHAPE-seq -
2
remove duplicete reads as icshape pipeline
SHAPE-seq -
3
trimmed reads adaptor as icshape pipeline
SHAPE-seq -
4
mapping reads to human hg38 or mouse mm10 reference genome with STAR as default parameters
STAR -
5
calculate rpkm as icshape pipeline
SHAPE-seq -
6
calulate reverse transcript stop sites as icshape-pipe
SHAPE-seq -
7
calculate icSHAPE score as icshape-pipe
SHAPE-seq
Raw Source Text
Library strategy: icSHAPE remove duplicete reads as icshape pipeline trimmed reads adaptor as icshape pipeline mapping reads to human hg38 or mouse mm10 reference genome with STAR as default parameters calculate rpkm as icshape pipeline calulate reverse transcript stop sites as icshape-pipe calculate icSHAPE score as icshape-pipe Genome_build: hg38 and mm10 Supplementary_files_format_and_content: tab-delimited text files for icshape files. First column is the Ensemble ID, second is gene length, third is *, then every column is the nucleotide resolution icSHAPE score. NULL means no confident score.