I met some problems when running the Rscript of Giremi (for Drosophila melanogaster RNA-seq data):
(1) The major_base column is all N;
(2) The pvalue_MI column is all -1, or sometimes with a few zero.
(3) The ifRNAE column is all 0.
These cause the abortion in the "ids = which(dat[,"major_base"]=="N") if (length(ids)>0) dat = dat[-ids,]" step and "pvalue_MI>0 & pvalue_MI <= 0.01" step.
Thus the dat.pos, dat.neg and dat.unknown files are all empty.
I have read the instructions and comments in these pages, and it doesn't seem to be the problem of the "list file",
2L 5091 5092 Inte 1 +
2L 5094 5095 Inte 1 +
2L 5371 5372 Inte 1 +
2L 5389 5390 Inte 1 +
2L 5402 5403 Inte 1 +
The SNP sites were called from GATK with strict criteria, and I have tried to set the $5 to be 0 or 1, and got the same problems.
I have also tried both single-end and pair-end libraries, and the same problems occurred.
I wonder what I should do to make the script run? I just want to get the list of editing sites in each library.
Hi, Qing,
I met some problems when running the Rscript of Giremi (for Drosophila melanogaster RNA-seq data): (1) The major_base column is all N; (2) The pvalue_MI column is all -1, or sometimes with a few zero. (3) The ifRNAE column is all 0.
These cause the abortion in the "ids = which(dat[,"major_base"]=="N") if (length(ids)>0) dat = dat[-ids,]" step and "pvalue_MI>0 & pvalue_MI <= 0.01" step. Thus the dat.pos, dat.neg and dat.unknown files are all empty.
I have read the instructions and comments in these pages, and it doesn't seem to be the problem of the "list file", 2L 5091 5092 Inte 1 + 2L 5094 5095 Inte 1 + 2L 5371 5372 Inte 1 + 2L 5389 5390 Inte 1 + 2L 5402 5403 Inte 1 +
The SNP sites were called from GATK with strict criteria, and I have tried to set the $5 to be 0 or 1, and got the same problems. I have also tried both single-end and pair-end libraries, and the same problems occurred.
I wonder what I should do to make the script run? I just want to get the list of editing sites in each library.
Thanks !