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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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IfRNAE Column not generating #5

Open BramUni opened 8 years ago

BramUni commented 8 years ago

I have been trying to run Giremi but I cant't seem to figure out how to get it to work properly. In my output everything seems fine as far as I can tell but there is no "IfRNAE" column and no "RNAE_t" column. I'm a bit new to the subject so please excuse if I'm making some huge mistake.

I'm running Giremi with a fasta ref file from GRC the first line looks like this:

1 dna:chromosome chromosome:GRCh37:1:1:249250621:1

The RNA_seq data that is the bam file inserted into Giremi I received from my professor it looks like this: head_of_RNA-seq.txt

The SNV file I'm using I created from what I believe to be a standard SNP data set, that file is called dbsnp_142.GRCh38.vcf, but in this file there were no gene names mentioned but everything else required of this input file seemed to be present. As I'm new to this subject the fact that this data is missing in this file makes me wonder if I'm not making some huge misinterpretation of how to use this file.

The output I get from Giremi is: head_out.txt and the tekst: [mpileup] 1 samples in 1 input files meanMI:0.007311 sdMI:0.017326

Thank you in advance.

best, Bram

doughertyr commented 8 years ago

Bram,

I noticed in your output file all bases are N's. Check out the "N's in output file" thread and see if any of the problems mentioned are relevant to your case.

Bobby

zhqingit commented 8 years ago

Hi Bram,

I guess the chromosome name in your fasta file is not same to that in your SNV list file. Please maker sure they are exactly same. It's better use chr1, chr2...

Best, Qing

2016-02-24 1:37 GMT-07:00 BramUni notifications@github.com:

I have been trying to run Giremi but I cant't seem to figure out how to get it to work properly. In my output everything seems fine as far as I can tell but there is no "IfRNAE" column and no "RNAE_t" column. I'm a bit new to the subject so please excuse if I'm making some huge mistake.

I'm running Giremi with a fasta ref file from GRC the first line looks like this:

1 dna:chromosome chromosome:GRCh37:1:1:249250621:1

The RNA_seq data that is the bam file inserted into Giremi I received from my professor it looks like this: head_of_RNA-seq.txt https://github.com/zhqingit/giremi/files/144119/head_of_RNA-seq.txt

The SNV file I'm using I created from what I believe to be a standard SNP data set, that file is called dbsnp_142.GRCh38.vcf, but in this file there were no gene names mentioned but everything else required of this input file seemed to be present. As I'm new to this subject the fact that this data is missing in this file makes me wonder if I'm not making some huge misinterpretation of how to use this file.

The output I get from Giremi is: head_out.txt https://github.com/zhqingit/giremi/files/144138/head_out.txt and the tekst: [mpileup] 1 samples in 1 input files meanMI:0.007311 sdMI:0.017326

Thank you in advance.

best, Bram

— Reply to this email directly or view it on GitHub https://github.com/zhqingit/giremi/issues/5.