Learn how to analyze unexpected splicing with STAR, including identifying novel junctions, validating findings, and understanding biological implications.
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Overview of Unexpected Splicing in STAR
Initial Setup and Alignment
STAR --runThreadN 8 --genomeDir /path/to/genome --readFilesIn /path/to/reads.fastq --outFileNamePrefix /output/path/prefix\_ --outSAMtype BAM SortedByCoordinate
Review STAR Outputs
Log.final.out
file for alignment statistics, which includes splice junction information. High numbers of uniquely mapped reads relative to multi-mapped reads indicate reliable results.
SJ.out.tab
file, which contains splice junctions identified by STAR. This file provides chromosome location, junction start and end, and evidence of annotation support.
Identify Unannotated Junctions
SJ.out.tab
with known annotations using computational tools or custom scripts to distinguish novel junctions from annotated ones.
Validate Unexpected Junctions
Interpret Results in Biological Context
Report and Document Findings
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