RNASeqTools

Some small tools to help with RNA-seq analysis

Installation

pip install git+ssh://git@github.com/SouthernCD/RNASeqTools.git

Usage

GetGeneLength

Get gene model (longest mRNA) length from GFF file

RNASeqTools GetGeneLength [-h] gff_file gene_length_file

positional arguments:
  gff_file          a gff file
  gene_length_file  gene length file (output)

optional arguments:
  -h, --help        show this help message and exit

Count2TMM

Give me a matrix of count. I can convert him into a TMM, FPKM and TPM matrix.

To get the TMM matrix, I depend on a perl script named run_TMM_scale_matrix.pl from Trinity, so you need to install Trinity first and make sure run_TMM_scale_matrix.pl is in your PATH.

RNASeqTools Count2TMM [-h] count_matrix gene_length_file output_prefix

positional arguments:
  count_matrix      a count matrix, row is gene, column is sample, mast have header in tsv format
  gene_length_file  gene length file, two columns, first is gene name, second is gene length
  output_prefix     output prefix, you will get output_prefix.TMM.matrix, output_prefix.fpkm.matrix and output_prefix.tpm.matrix

optional arguments:
  -h, --help        show this help message and exit

DenovoCount2RefCount

Sometimes we want to map the expression information obtained from de novo transcriptome assembly data to a reference genome of a closely related species, and DenovoCount2RefCount helps you do that!

RNASeqTools DenovoCount2RefCount [-h] [-f REF_GENOME_FASTA] [-g REF_GENOME_GFF] [-c REF_CDNA_FASTA] [-o WORK_DIR] [-m MAP_PROGRAM] de_novo_fasta de_novo_trans_gene_map rsem_gene_results

positional arguments:
  de_novo_fasta         a fasta file from trinity output
  de_novo_trans_gene_map
                        a gene_trans_map file from trinity output
  rsem_gene_results     a rsem gene results file

optional arguments:
  -h, --help            show this help message and exit
  -f REF_GENOME_FASTA, --ref_genome_fasta REF_GENOME_FASTA
                        refernce genome fasta
  -g REF_GENOME_GFF, --ref_genome_gff REF_GENOME_GFF
                        refernce genome gff
  -c REF_CDNA_FASTA, --ref_cDNA_fasta REF_CDNA_FASTA
                        refernce cDNA fasta, if not given, will use ref_genome_fasta and ref_genome_gff, only work for blast
  -o WORK_DIR, --work_dir WORK_DIR
                        work dir
  -m MAP_PROGRAM, --map_program MAP_PROGRAM
                        map program, blat or blast

Example

DenovoCount2RefCount

Mapping trinity results and rsem results to a reference genome using blat

RNASeqTools DenovoCount2RefCount -f ref_genome.fna -g ref_genome.gff -o map_out -m blat Trinity.fasta Trinity.fasta.gene_trans_map rsem.genes.results

Mapping trinity results and rsem results to a reference genome cDNA using blast

RNASeqTools DenovoCount2RefCount -c ref_cDNA.fna -o map_out -m blast Trinity.fasta Trinity.fasta.gene_trans_map rsem.genes.results

GetGeneLength

RNASeqTools GetGeneLength gene_model.gff gene_length.tsv

Count2TMM

RNASeqTools Count2TMM count_matrix.tsv gene_length.tsv output_prefix