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guigolab / sqtlseeker2-nf

An automated sQTL mapping pipeline using Nextflow
GNU General Public License v3.0
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No transcripts with expression above threshold #5

Open dfermin opened 2 years ago

dfermin commented 2 years ago

Hello. I'm trying to analyze my data with sqtlseeker2-nf. Whenever I run the tool with my data I get this error message:


Caused by:
  Process `prepare (all)` terminated with an error exit status (1)

Command executed:

  prepare_trexp.R --group "all" -t transExpression.v2.tsv -m metadata.tsv --gene_location genes.bed --output_tre tre.df.RData --output_gene genes.ss.bed --output_cov covariates.df.RData

Command exit status:
  1

Command output:
  (empty)

Command error:
  Error in prepare.trans.exp(te.df, min.gene.exp = opt$min_gene_expr, min.transcript.exp = opt$min_transcript_expr,  :
    No transcripts with expression above threshold
  Execution halted

My dataset is human RNAseq data for 230 samples. The transcript data is in FPKM (not scaled or transformed). I've filtered the data to include only genes with > 1 transcript. In addition, I am only keeping transcripts with a relative expression > 0.01 (relative to the total expression for the gene).

Do you have any suggestions for what might be wrong?

Thanks, Damian

dgarrimar commented 2 years ago

Filters on gene expression and transcript expression are set on absolute (not relative) values, in your case, directly in FPKM. Still, it is strange that any of your transcripts is above the threshold. Make sure you are setting the right thresholds and check out the input formats. If the problem persists, please provide some test data so that we can replicate the problem.