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mrnaScan

The Python toolkits designed to identify exons and 3'UTR of each reads for bulk/single-cell full-length mRNA-seq

Installation

python3 -m pip install --upgrade mrnaScan

Usage

# Basic usage
mrnaScan [options] -i <input.bam> -r <reference.gtf>

# For more information
mrnaScan -h

Output

  • *_exon_info.h5: a hdf5 file include count table of pesudo-transcripts and their exon information
  • *_utr_info.tsv: a tab-separated table of 3'utr length of each gene

Features

  • The exons and 3'utr of each reads
  • The pesudo-transcripts defined via the combination of exons
  • The count table of pesudo-transcripts
  • Other feature would be supported in the future ...