estimate

ESTIMATE provides researchers with scores for tumor purity, the level of stromal cells present, and the infiltration level of immune cells in tumor tissues based on expression data

Dependencies

• estimate 1.0.13
• rstats 4.0

Usage

Cromwell

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

Inputs

Required workflow parameters:

Parameter	Value	Description
inputData	Array[Pair[File,File]]+	Input files with the first and second mate reads.
launchEstimate.estimateScript	String	Script to run ESTIMATE
launchEstimate.rsemZscoreRScript	String	calculation of zScore for ESTIMATE results
launchEstimate.ensFile	String	file for converting Ensembl gene_id to HUGO symbol

Optional workflow parameters:

Parameter	Value	Default	Description
outputFileNamePrefix	String	"ESTIMATE"	Output prefix, customizable. Default is the first file's basename.

Optional task parameters:

Parameter	Value	Default	Description
preProcessRsem.jobMemory	Int	8	Memory allocated to the task.
preProcessRsem.timeout	Int	20	Timeout in hours, needed to override imposed limits.
preProcessRsem.tmpDir	String	"tmp"	temporary directory
preProcessRsem.dataDir	String	"data"	data directory
launchEstimate.jobMemory	Int	8	Memory allocated to the task.
launchEstimate.timeout	Int	20	Timeout in hours, needed to override imposed limits.
launchEstimate.dataDir	String	"."	data directory
launchEstimate.modules	String	"estimate/1.0.13"	Names and versions of required modules. This needs to be customized by shesmu

Outputs

Output	Type	Description	Labels
gRcounts	File	File with RAW counts	vidarr_label: gRcounts
gCounts	File	File with estimated counts	vidarr_label: gCounts
gFpkm	File	FPKMS from RSEM	vidarr_label: gFpkm
gTpm	File	TPMS from RSEM	vidarr_label: gTpm
estimateFile	File	File with results from ESTIMATE	vidarr_label: estimateFile

Commands

This section lists command(s) run by estimate workflow

• Running ESTIMATE

Merge data

Bash code is used to extract data from RSEM and STAR inputs into separate tables for TPMs, FPKMs and counts.

 
 TMP='~{tmpDir}'
 DATA='~{dataDir}'
 mkdir $TMP
 mkdir $DATA
 
 cp ~{sep=' ' rsemData} $DATA/
 cp ~{sep=' ' starData} $DATA/
 
 STARG=$(ls $DATA/*.tab | head -1);
 if [ ! -z $STARG ]; then
   awk 'NR>3 {print $1}' $STARG | sed 's/N_ambiguous/gene_id/' > $TMP/sgene;
 fi;
 
 RSEMG=$(ls $DATA/*.genes.results | head -1);
 if [ ! -z $RSEMG ]; then
   cut -f 1 $RSEMG  > $TMP/genes;
 fi;
 
 # We will use basename as a sample ID here
 for t in $DATA/*results;do
   BASE=$(basename $t | sed s/.results$//);
   NAME=$(echo $BASE | sed 's/\..*//');
   echo $t;
   echo $NAME > $TMP/$NAME.fpkm;
   cut -f 7 $t | awk 'NR>1' >> $TMP/$NAME.fpkm;
   echo $NAME > $TMP/$NAME.tpm;
   cut -f 6 $t | awk 'NR>1' >> $TMP/$NAME.tpm;
   echo $NAME > $TMP/$NAME.count;
   cut -f 5 $t | awk 'NR>1' >> $TMP/$NAME.count;
   echo $NAME > $TMP/$NAME.rcount;
   awk 'NR>4 {if ($4 >= $3) print $4; else print $3}' $DATA/$NAME.ReadsPerGene.out.tab >> $TMP/$NAME.rcount;
 done
 
 # Merging
 paste $TMP/sgene $TMP/*.rcount > ~{outputPrefix}_genes_all_samples_RCOUNT.txt;
 paste $TMP/genes $TMP/*.count > ~{outputPrefix}_genes_all_samples_COUNT.txt;
 paste $TMP/genes $TMP/*.fpkm > ~{outputPrefix}_genes_all_samples_FPKM.txt;
 paste $TMP/genes $TMP/*.tpm > ~{outputPrefix}_genes_all_samples_TPM.txt;

Run ESTIMATE using FPKM values

  set -euo pipefail
  Rscript ~{estimateScript} ~{inRSEM} ~{dataDir} ~{ensFile} ~{rsemZscoreRScript} ~{outputFileNamePrefix}

Support

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

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