cuffdiff outputs empty "" file - and readCufflinks() complains
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4.4 years ago
murraym • 0

Hi, We are analysing an RNAseq experiment using cuffquant and then cuffdiff on the resultant .cxb files, and then trying to load the data in R using the "readCufflinks" command in the cummeRbund package. readCufflinks() fails and writes an error message saying the file has no lines. is indeed empty, as are several other files in the cuffdiff output directory, but there are also other files that look fine (e.g. "gene_exp.diff"), so we are not sure if those empty files are normal. We suspect not, since cuffdiff eventually crashes with a segmentation fault 11 (just after printing "Writing run info"). Any suggestions as to what might be wrong would be appreciated. The commands used are below. thanks, Mike

here's the R command.

cuff<-readCufflinks() Creating database /Users/fred/Desktop/cuffdiff_output_dir/ Error in (function (file, header = FALSE, sep = "", quote = "\"'", dec = ".", : no lines available in input In addition: There were 50 or more warnings (use warnings() to see the first 50)

and here are the Unix commands.

cuffquant -o ./Ctl5A_quant -p4 ~/Desktop/Genome/gencode.v21.annotation.gtf ./Ctl5A/accepted_hits.bam cuffquant -o ./Ctl5B_quant -p4 ~/Desktop/Genome/gencode.v21.annotation.gtf ./Ctl5B/accepted_hits.bam cuffquant -o ./Ctl5C_quant -p4 ~/Desktop/Genome/gencode.v21.annotation.gtf ./Ctl5C/accepted_hits.bam cuffquant -o ./Exp5A_quant -p4 ~/Desktop/Genome/gencode.v21.annotation.gtf ./Exp5A/accepted_hits.bam cuffquant -o ./Exp5B_quant -p4 ~/Desktop/Genome/gencode.v21.annotation.gtf ./Exp5B/accepted_hits.bam cuffquant -o ./Exp5C_quant -p4 ~/Desktop/Genome/gencode.v21.annotation.gtf ./Exp5C/accepted_hits.bam

cuffdiff ~/Desktop/Genome/gencode.v21.annotation.gtf -o ./cuffdiff_output_dir Ctl5A_quant/abundances.cxb,Ctl5B_quant/abundances.cxb,Ctl5C_quant/abundances.cxb Exp5A_quant/abundances.cxb,Exp5B_quant/abundances.cxb,Exp5C_quant/abundances.cxb

RNA-Seq cuffdiff cummeRbund readCufflinks • 1.5k views
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Directory name missing in cuff<-readCufflinks( dir=?).


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