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✒️SRA-RNAseq

Our Guthub repo include pipelines for running Pre-processing methods such as Trimming, quality control and pseudoalignment on SRA fastq files using Trimmomatic, fastQC and Kallisto tools respectively. All the pipelines are written using the Workflow Description Language (WDL) and can be executed using Cromwell and Docker.

⚙️Technologies & Tools

🔗 Quick Start

SRA fastq files download

  • Install SRAtoolkit
  • Run the following command to download SRA fastq files in parallel. The list.txt includes SRA ids.

parallel --jobs n "fastq-dump --split-files --skip-technical -B --gzip {}" :::: list.txt

Running Trim-QC & Kallisto pipeline in WDL format

  • Install JAVA, and Cromwell
  • Build Docker images for Trimmomatic, fastQC and Kallisto
  • For running Kallisto.wdl you also need to build an index from a FASTA formatted file of target sequences using Kallisto and name it under gencode.idx.
  • Run the workflow directly by executing the following commands on your terminal:

java -Dconfig.file=application.conf -jar cromwell-55.jar run Trim-QC.wdl -i Trim-QC.json

java -Dconfig.file=application.conf -jar cromwell-55.jar run Kallisto.wdl -i Kallisto.json