😲 Goosebumps paired-end RNA-Seq pipeline

RNA_Seq Python Pipeline :copyright:ABCLab Jongheon Lee

☑️ requirement : python3 Fastqc Trimmomatic Star featureCounts , and *.fastq files

Biopython, gzip, wget, getopt

✔️ Notice : *.fastq files must be located in the same directory with option -p /Path/

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• example command (SRR390728)

  python3 pipeline.py -v 104 -s mus_musculus -i GRCm39 -p /disk1/bijh/10.Circadian_Transcriptome/ --tdir /program/Trimmomatic/ --th 32 --tver TruSeq3-PE.fa --mode genomeGenerate --T 4 

• To Download reference files

  -v <Ensembl version>
  -s <Scientific Name>
  -i <Ref version >
  -p </PATH/> where fastq files located

• To launch Pipeline tools

  --tdir <PATH> TRIMMOMATIC TOOL PATH
  --th <int> Number of Thread
  --tver <Adapter Ver.>
  --mode <STAR Mode> (default alignReads)
  --T <int> Number of CPU Core for featureCounts

pipeline.py

• this is the main script file.

getFiles.py

• Download reference files on Ensembl DB through wget.
• Other functions definition.

fastqc.py

• To build fastq.html files for the read files's quality check.

trimmomatic.py

• Trimming read files and get 4 outputfiles (forward_paired, forward_unpaired, reverse_paired, reverse_unpaired)
  • removing adapters... adapter options required

starindexing.py

• alignment step
  • indexing fa file (reference file)

starmapping.py

• mapping seq files to gtf file
  • output data type is sorted bam

FeatureCount.py

• check expression rate