transgram Files

TransGram Image Usage Guide

TransGram is a genome-guided transcriptome reconstruction tool designed for long RNA-seq reads.It provides accurate transcriptome assembly and analysis capabilities for long-read sequencing technologies.

Image Files Description

This directory contains two TransGram image files:

trans_gram-20250912.sif - Singularity image file

trans_gram-20250912.tar - Docker image archive file

Using Docker Image

Step 1: Load Docker Image

docker load -i $dockerimage_path/trans_gram-20250912.tar

Step 2: Run TransGram Container

docker run --rm -v $(pwd):/data trans_gram:20250912 /TransGram/TransGram -b /data/SRR14181741_1.bam -o /data/transgram_outdir

Help Information

docker run --rm trans_gram:20250912 /TransGram/TransGram --help

Parameter Explanation:

--rm: Automatically remove the container after exit

-v $(pwd):/data: Mount the current directory to the container's /data directory

-b /data/SRR14181741_1.bam: Specify the input BAM file path (mounted inside the container)

-o /data/transgram_outdir: Specify the output directory path (mounted inside the container)

Using Singularity Image

singularity exec trans_gram-20250912.sif /TransGram/TransGram -b SRR14181741_1.bam -o transgram_outdir

For more support or questions regarding TransGram usage, please visit our GitHub repository TransGram.