RNA-seq

RNake

Bacterial RNA-seq trimming, mapping and count-table generation workflow.

STATUS: TEST IN PROGRESS

Pipeline Flow

Prefilter→ Trim→ Bowtie2 Mapping→ Count Matrix→ Merged Table

Build

cd RNake
docker build -t rnake:latest .

Run

./RNake/Go_Rnake.sh \
  -i /path/to/reads \
  -o project_name \
  -g /path/to/genome.fna \
  -a /path/to/annotation.gff \
  -K

Real Example

Go_Rnake.sh \
  -i RNake/20261101_RNA_HKP \
  -o RNake/20261101_RNA_HKP_out \
  -g /media/uhlemann/Core3_V2/REF/ecoli.fna \
  -a /media/uhlemann/Core3_V2/REF/ecoli.gff \
  -K

Options

FlagDescription
-nDry-run
-KKeep-going
-cSnakemake cores

Expected Input

RNake/
|-- 20251101_RNA_HKP/
|-- 20251101_RNA_HKP_out/
|-- 20261101_RNA_HKP/
|   |-- SAMPLE1_R1.fastq.gz
|   `-- SAMPLE1_R2.fastq.gz
`-- 20261101_RNA_HKP_out/

RNA_ref/
|-- ecoli.fna
`-- ecoli.gff

Main Outputs

RNake/
|-- 20251101_RNA_HKP/
|-- 20251101_RNA_HKP_out/
|-- 20261101_RNA_HKP/
`-- 20261101_RNA_HKP_out/
    |-- 1_trim/
    |-- 3_bowtie2_files/
    |-- 5_counts/
    `-- merged_counts_with_gene_names.csv