Hello,

I am trying to setup the DROP pipeline by Gagneur lab.

The goal is to detect outliers in a Bulk RNA-seq sample of 1 affected individual. I don't have a control so I am trying to use th publicly available external counts file given on DROP's documentation. I am able to run the demo data. So the tool is setup properly. However when I edit the sample annotation file (I am looking at only the aberrant expression pipeline) for my purpose it seems to cause errors. Has anyone tried DROP for this purpose? Any other methods recommended when only 1 affected sample is available?

This is a short test version of my sample annotation file with 1 affected individual and 10 external counts.

RNA_ID  RNA_BAM_FILE    DNA_ID  DROP_GROUP  PAIRED_END  COUNT_MODE  COUNT_OVERLAPS  STRAND  

DNA_VCF_FILE    GENE_COUNTS_FILE    GENE_ANNOTATION GENOME 
HG00096 /projectnb/4kajdatx/drop-1.3.4/Data/rna_bam/HG00096_ncbi.bam    HG00096 blood   TRUE    IntersectionStrict  TRUE    no  /projectnb/4kajdatx/drop-1.3.4/Data/dna_vcf/demo_chr21_ncbi.vcf.gz      gencode34   hg19 
WB100000            blood   TRUE    IntersectionStrict  TRUE    no      /projectnb/4kajdatx/drop_ctrl/blood--hg19--gencode34/geneCounts.tsv.gz  gencode34   hg19 
WB100001            blood   TRUE    IntersectionStrict  TRUE    no      /projectnb/4kajdatx/drop_ctrl/blood--hg19--gencode34/geneCounts.tsv.gz  gencode34   hg19 WB100002           blood   TRUE    IntersectionStrict  TRUE    no      /projectnb/4kajdatx/drop_ctrl/blood--hg19--gencode34/geneCounts.tsv.gz  gencode34   hg19 
WB100003            blood   TRUE    IntersectionStrict  TRUE    no      /projectnb/4kajdatx/drop_ctrl/blood--hg19--gencode34/geneCounts.tsv.gz  gencode34   hg19 WB100004           blood   TRUE    IntersectionStrict  TRUE    no      /projectnb/4kajdatx/drop_ctrl/blood--hg19--gencode34/geneCounts.tsv.gz  gencode34   hg19 
WB100005            blood   TRUE    IntersectionStrict  TRUE    no      /projectnb/4kajdatx/drop_ctrl/blood--hg19--gencode34/geneCounts.tsv.gz  gencode34   hg19 WB100006           blood   TRUE    IntersectionStrict  TRUE    no      /projectnb/4kajdatx/drop_ctrl/blood--hg19--gencode34/geneCounts.tsv.gz  gencode34   hg19 
WB100007            blood   TRUE    IntersectionStrict  TRUE    no      /projectnb/4kajdatx/drop_ctrl/blood--hg19--gencode34/geneCounts.tsv.gz  gencode34   hg19 WB100008           blood   TRUE    IntersectionStrict  TRUE    no      /projectnb/4kajdatx/drop_ctrl/blood--hg19--gencode34/geneCounts.tsv.gz  gencode34   hg19 
WB100009            blood   TRUE    IntersectionStrict  TRUE    no      /projectnb/4kajdatx/drop_ctrl/blood--hg19--gencode34/geneCounts.tsv.gz  gencode34   hg19 WB100010           blood   TRUE    IntersectionStrict  TRUE    no      /projectnb/4kajdatx/drop_ctrl/blood--hg19--gencode34/geneCounts.tsv.gz  gencode34   hg19

Is there a different recommended approach?

Thank you