Error in data.table::setnames: 'old' is length 7 but 'new' is length 2

[deb0612]

Dear sir, when I tried to apply RNAseqCNV either by shinnyapp or by command, it show the error message below: My read counts was generated from featurecounts. "command: featureCounts -T 10 -a GENCODE28.gtf -o read.count -p -B -C -f -t exon -g gene_id *.bam" Is that the wrong format of my GTF file?

[honzee]

Hi,

thank you for trying out our package!

I think this might be caused by incorrectly formatted counts file. It is expected to have two columns (https://github.com/honzee/RNAseqCNV#213-read-count-file-), but I think your has 7. Could you send the first few lines for your counts file to validate this?

If this is the case, I would suggest to reformat the input count files.

Best, Jan

[deb0612]

The count file looked like this: Geneid Chr Start End Strand Length A2969_S226_L003.pb.hg38.bam ENSG00000223972.5 1 11869 12227 + 359 0 ENSG00000223972.5 1 12613 12721 + 109 0 ENSG00000223972.5 1 13221 14409 + 1189 1 ENSG00000223972.5 1 12010 12057 + 48 0 ENSG00000223972.5 1 12179 12227 + 49 0 ENSG00000223972.5 1 12613 12697 + 85 0 ENSG00000223972.5 1 12975 13052 + 78 1 ENSG00000223972.5 1 13221 13374 + 154 0

[deb0612]

I tried to reformat my count file, however there are other problem

[honzee]

Could you test it in console using the wrapper function - we might get more information that way. Also, could you please send the header of one of the count files again? It seems they are not being read correctly.

Best, Jan

[deb0612]

In console

header of count file

[honzee]

Looking again at the count data matrix, the ensemble IDs are not correctly formatted. RNAseqCNV expects unique ensemble gene ids but multiple rows have the same ensemble id.

I suggest collapsing all rows with the same ensemble id together.

Best, Jan