Hello! I'm processing samples with multiple replicates, and I've found that the system works fine as long as the number of treated and untreated samples is the same. But in many cases, I have a single mock file and 2-8 treated samples.
I've tried setting my command script up with tsamp = "T1name, T2name, T3name..." and usamp = "U1name", but each time the pipeline gets stuck during overlap analysis:
"################ DELTA AND HITS ################ "
"CAST0CCR5OT0WTRNP0DUP_S1_L001 vs. CAST0CCR5OT0MOCK_S1"
"Error: File not found -> ../samples/CCR5_OT_WTRNP/U2/fastq_aln/CAST0CCR5OT0MOCK_S1_Alignment.bed"
"################ OVERLAP ANALYSIS ################"
"../samples/CCR5_OT_WTRNP/OVL2_SIGNIF1"
Error in read.xlsx.default(X[[i]], ...) : File does not exist.
Calls: runPipelineCRISPR ... getUnion -> lapply -> lapply -> FUN -> read.xlsx.default
Execution halted
I can get around this by simply duplicating the U1 file and changing the name slightly, but it massively increases the processing time because it treats each untreated file as a distinct sample. Is there a simpler way to do this?? Thank you!
Hello! I'm processing samples with multiple replicates, and I've found that the system works fine as long as the number of treated and untreated samples is the same. But in many cases, I have a single mock file and 2-8 treated samples.
I've tried setting my command script up with tsamp = "T1name, T2name, T3name..." and usamp = "U1name", but each time the pipeline gets stuck during overlap analysis:
"################ DELTA AND HITS ################ " "CAST0CCR5OT0WTRNP0DUP_S1_L001 vs. CAST0CCR5OT0MOCK_S1" "Error: File not found -> ../samples/CCR5_OT_WTRNP/U2/fastq_aln/CAST0CCR5OT0MOCK_S1_Alignment.bed"
"################ OVERLAP ANALYSIS ################" "../samples/CCR5_OT_WTRNP/OVL2_SIGNIF1" Error in read.xlsx.default(X[[i]], ...) : File does not exist. Calls: runPipelineCRISPR ... getUnion -> lapply -> lapply -> FUN -> read.xlsx.default Execution halted
I can get around this by simply duplicating the U1 file and changing the name slightly, but it massively increases the processing time because it treats each untreated file as a distinct sample. Is there a simpler way to do this?? Thank you!