TransGram is a genome-guided transcriptome reconstruction tool for long RNA-seq reads.

Additional Directories in TransGram

plugin/

This directory contains a simple tool used in the TransGram paper to extract transcripts based on the estimated transcript expression levels from third-party tools. Usage examples:

Getting the IsoQuant transcripts whose count larger than 1

filter_transcripts_based_on_count sample.transcript_model_counts.tsv sample.transcript_models.gtf Filter-1.gtf 1 isoQuant

Getting the Bambu transcripts whose CPM larger than 1

filter_transcripts_based_on_count CPM_transcript.txt extended_annotations.gtf Filter-1.gtf 1 Bambu

Getting the Espresso transcripts whose abundance larger than 1

filter_transcripts_based_on_count samples_N2_R0_abundance.esp samples_N2_R0_updated.gtf Filter-1.gtf 1 espresso

SimulateData/

This directory contains the scripts used for simulated data generation in the TransGram paper.

Docker/

This directory contains both the Docker image and the Singularity image for TransGram. Users can directly download and use the image.

Alternatively, users may install TransGram from source by cloning the TransGram GitHub repository and run:

  $ make all release
  $ TransGram -b alignment.bam -o transgram_outdir

Subsampling experiments on Nanopore RNA sequencing data/

This directory contains code and data for generating Beta-type subsets from the Nanopore sequencing dataset R6.

The /beta_type_subsets directory contains Beta-type subsets derived from the Alpha-type Nanopore sequencing dataset R6.

For subsampling instructions, please refer to Subsampling_experiments_on_Nanopore_RNA_sequencing_data/README.md.