ercc

Ercc 1.1, Niassa-wrapped Cromwell (widdle) workflow for running ERCC spike-in analysis on RNAseq data. The workflow counts total reads in fastq files, evaluate expression of ERCC spike-ins using bwa aligner and creates a report in .json format, along with plots in .png and .pdf formats. The .json file contains RPKMs for all ERCC transcripts as well as other information. RPKM table in .csv format is also provisioned.

Overview

Dependencies

• rstats 4.0
• bwa 0.7.17
• samtools 0.1.19

Usage

Cromwell

java -jar cromwell.jar run ercc.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter	Value	Description
fastqR1	File	File with reads for mate 1 or fastq file for single-read data
mixId	String	LIMS-approved identification of the Spike-In Mix
sampleId	String	The Id used to identify the data in the report
reference	String	hg19 or hg38 (assembly id)

Optional workflow parameters:

Parameter	Value	Default	Description
fastqR2	File?	None	File with reads for mate 2, is available
outputFileNamePrefix	String	basename(fastqR1,'.fastq.gz')	Prefix for the output file

Optional task parameters:

Parameter	Value	Default	Description
countTotal.jobMemory	Int	8	Memory allocated to this job
countTotal.timeout	Int	20	Timeout in hours for this task
countTranscripts.timeout	Int	20	Timeout in hours for this task
countTranscripts.jobMemory	Int	20	Memory allocated to this job
countTranscripts.threads	Int	8	Threads to use with bwa
countTranscripts.cnv_file	String	"ercc_counts.csv"	Output, contains ERCC ids and their respective number of reads
rpkmTable.timeout	Int	20	Timeout in hours for this task
rpkmTable.jobMemory	Int	10	Memory allocated to sort task
makeReport.imagingScriptPath	String	"$ERCC_SCRIPTS_ROOT/ercc_plots.R"	path to R script ercc_plots.R
makeReport.rScript	String	"$RSTATS_ROOT/bin/Rscript"	Path to Rscript command
makeReport.jobMemory	Int	10	Memory allocated to classify task

Outputs

Output	Type	Description	Labels
rpkmData	File	ERCC readouts in RPKMs	vidarr_label: rpkmData
image	File	png with a plot (Dose Response supported at the moment)	vidarr_label: image
pdf	File	pdf with the same plot as png, a legacy output	vidarr_label: pdf
json	File	json file with ERCC numbers	vidarr_label: json

Commands

This section lists command(s) run by ercc workflow

• Running ercc

ercc workflow checks out spike-in signal (reads) and plots the QC graph(s).

Count reads in fastq file:

   zcat FASTQ_R1 | paste - - - - | wc -l  
 

Align reads to chimeric reference (modified reference also containing all spike-in sequences)

   bwa mem -t THREADS -M REF_GENOME FASTQ_R1 FASTQ_R2 | samtools view -S - | 
       cut -f 3 | grep ERCC | sort | uniq -c | sed s/^\ *// > CNV_FILE

In this custom script we build the RPKM table

  python <<CODE
  import os
  ercc = os.path.expandvars("~{erccData}")
  counts = "~{erccCounts}"
  total = ~{totalReads}
  output_file = "~{basename(erccCounts, '.csv')}_rpkm.csv"
 
  # 1. Open file, read and collect length data
  ercc_data = open(ercc, 'r')
  length_hash = {}
  for nextLine in ercc_data.readlines():
      nextFields = nextLine.split("\t")
      length_hash[nextFields[0]] = int(nextFields[4])
  ercc_data.close()
 
  # 2. Calculate RPKMs, put them in a hash
  count_data = open(counts, 'r')
  rpkm_hash = {}
  count_hash = {}
 
  for nextLine in count_data.readlines():
      nextLine = nextLine.strip("\n")
      countChunk = nextLine.split(" ")
      if len(countChunk) == 2 and countChunk[1] in length_hash.keys():
          count_hash[countChunk[1]] = int(countChunk[0])
 
  pm = int(total)/1000000.0
  for e in sorted(length_hash.keys()):
     rpkm = 0.0
     if e in count_hash.keys():
         rpkm = count_hash[e]/pm/(length_hash[e]/1000.0)
     rpkm_hash[e] = "{0:.2f}".format(rpkm)
  count_data.close()
 
  # 3. print out RPKMS sorted by
  f = open(output_file, "w+")
  for e in sorted(rpkm_hash.keys()):
      f.write('\t'.join([e, rpkm_hash[e]]) + '\n')
  f.close()
  CODE
 

Report Making using oputputs from the other steps:

  Rscript IMAGING_SCRIPT RPKM_TABLE CONTROL_DATA ERCC_DATA PREFIX DoseResponse SAMPLES

Support

For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .

Generated with generate-markdown-readme (https://github.com/oicr-gsi/gsi-wdl-tools/)