Running ScanMST¶

Learn how to perform multi-segment transcript identificaiton with ScanMST.

Learning Objectives

By the end of this tutorial, you will be able to:

Necesary files preparation
Run ScanMST generation

Prerequisites:

ScanMST installed
BAM file prepared, see the Reads Alignment Tutorial.
Basic command-line experience

Time: Approximately 30 minutes to several hours, depending on the size of the BAM file

Necessary files preparation¶

# Download reference genome FASTA
wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
gunzip hg38.fa.gz

# Download reference genome 2bit file
wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit

# Download reference annotation GTF
wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_48/gencode.v48.annotation.gtf.gz
gunzip gencode.v48.annotation.gtf.gz

Begin to run ScanMST¶

scanmst --thread 1 --input sample.bam --output sample --ref hg38.fa --gtf gencode.v48.annotation.gtf --ncan --aligner blat --blat-2bit hg38.2bit --blat-port 88890 --log-level debug --graph --refine &> sample.log

Expected Output¶

GTF: Store transcript segments (detailed exons) and segment links.
VCF: Aggregated segment links by positions
FASTA: Consensus transcript sequences
JSON: Transcript segment graph

Summary¶

You've learned how to:

✅ Prepare necessary files for ScanMST
✅ Run ScanMST to identify MSTs.

Identified MSTs Data Ready!

The MSTs identified are now ready for high-quality downstream analysis!