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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 in data.frame #24

Closed Lsteenhuis closed 7 years ago

Lsteenhuis commented 7 years ago

Dear Qing,

I have been trying to get giremi running over the past few weeks, and used the issues on this page to try to solve my problems. But now I have the following error:

dat.pos <- cbind(dat.pos[,c("upstream_1base","downstream_1base")],abs(dat.pos[,"major_ratio"]-dat.pos[,"estimated_allelic_ratio"]),1) Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 0, 1 Calls: cbind -> cbind -> data.frame Execution halted

I have seen you suggest to remove the homozygous SNV's from the list, I think I have done this correctly but the error persists. The output files and my list of SNV's are attached and I would greatly appreciate it if you could take some of your time to help me figure out this problem.

giremi_out.txt giremi_out.vcf.Rout.txt test_snps.txt

Cheers,

Lars

zhqingit commented 7 years ago

Hi Lars,

When you run giremi, you can see the meanMI and sdMI in the screen, could you send me the two values? Thanks.

Best, Qing

2016-10-10 1:41 GMT-07:00 Lsteenhuis notifications@github.com:

Dear Qing,

I have been trying to get giremi running over the past few weeks, and used the issues on this page to try to solve my problems. But now I have the following error:

dat.pos <- cbind(dat.pos[,c("upstream_1base","downstream_1base")], abs(dat.pos[,"major_ratio"]-dat.pos[,"estimated_allelic_ratio"]),1) Error in data.frame(..., check.names = FALSE) : arguments imply differing number of rows: 0, 1 Calls: cbind -> cbind -> data.frame Execution halted

I have seen you suggest to remove the homozygous SNV's from the list, I think I have done this correctly but the error persists. The output files and my list of SNV's are attached and I would greatly appreciate it if you could take some of your time to help me figure out this problem.

giremi_out.txt https://github.com/zhqingit/giremi/files/519046/giremi_out.txt giremi_out.vcf.Rout.txt https://github.com/zhqingit/giremi/files/519049/giremi_out.vcf.Rout.txt test_snps.txt https://github.com/zhqingit/giremi/files/519052/test_snps.txt

Cheers,

Lars

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Lsteenhuis commented 7 years ago

Hey Qing,

Thanks for the quick reaction, my meanMI and sdMI are:

meanMI:0.004893 sdMI:0.028364

It caught my eye that these values are really low. I have seen you suggest to use more stringent SNV calling, do you also suggest to increase the stringency of the filters?

Thanks in advance,

Lars

zhqingit commented 7 years ago

Hi Lars,

Yes, I think your SNP list is not pure, there must be many sequencing errors. So please try more strict filters.

Best, Qing

2016-10-11 7:38 GMT-07:00 Lsteenhuis notifications@github.com:

Hey Qing,

Thanks for the quick reaction, my meanMI and sdMI are:

meanMI:0.004893 sdMI:0.028364

It caught my eye that these values are really low. I have seen you suggest to use more stringent SNV calling, do you also suggest to increase the stringency of the filters?

Thanks in advance,

Lars

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/zhqingit/giremi/issues/24#issuecomment-252936304, or mute the thread https://github.com/notifications/unsubscribe-auth/ALL2zX94vwWjlNUgaTHFTlo1EWg1CG2Cks5qy59ZgaJpZM4KSVh5 .

Lsteenhuis commented 7 years ago

Hey Qing,

Alright I will play around some more, thanks for the help! I will close the threat since I know what to do now.

Cheers,

Lars