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zhqingit / giremi

GIREMI is a method that can identify RNA editing sites using one RNA-seq data set without requiring genome sequence data.
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Error while running giremi.r #8

Closed narangsign closed 8 years ago

narangsign commented 8 years ago

Hi Qing,

I am also getting error while running giremi.r:

Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 0, 1 Calls: cbind -> cbind -> data.frame Execution halted

I have attached my giremi output files. Please help!

giremi_output.Rout.txt

giremi_output.zip

zhqingit commented 8 years ago

Hi,

Your SNV list file includes only the homozygous SNPs.

Best, Qing

2016-03-14 23:12 GMT-07:00 Vipin notifications@github.com:

Hi Qing,

I am also getting error while running giremi.r:

Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 0, 1 Calls: cbind -> cbind -> data.frame Execution halted

I have attached my giremi output files. Please help!

giremi_output.Rout.txt https://github.com/zhqingit/giremi/files/173348/giremi_output.Rout.txt

giremi_output.zip https://github.com/zhqingit/giremi/files/173350/giremi_output.zip

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narangsign commented 8 years ago

Hi Qing,

Thanks for your prompt reply. Yes, most SNPs in my data are homozygous but a few are not. Will giremi not work for this type of dataset?

As others have also requested in the forum, can you please provide a set of sample input files for reference. It will help us a lot to check our data.

Best,

zhqingit commented 8 years ago

HI,

The homozygous SNPs can cause the MI calculation and allelic ratio estimation problems. Please remove them.

Please find the sample file in this issue: #4

Best, Qing

narangsign commented 8 years ago

Thanks, my question is answered. I am closing this thread.