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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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Question about SNV list #23

Open rz2333 opened 7 years ago

rz2333 commented 7 years ago

Hi qing,

I'm new to bioinformatics and I'm wondering how other users get the list of SNVs? I'm analyzing data from mouse and I could download dbSNPs information from UCSC. Thanks for your time!

Bests, Ray

zhqingit commented 7 years ago

Hi Ray,

You can get the list by using GATK or other SNV calling methods.

Best, Qing

2016-10-03 13:45 GMT-07:00 Rui Hong notifications@github.com:

Hi qing,

I'm new to bioinformatics and I'm wondering how other users get the list of SNVs? I'm analyzing data from mouse and I could download dbSNPs information from UCSC. Thanks for your time!

Bests, Ray

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zhqingit commented 7 years ago

Hi Ray,

GIREMI is designed to find the RNA editing sites from a mixture of the RNA editing sites and SNPs. I am not clear what's your purpose to input a file with all SNPs?

Best, Qing

2016-10-04 10:03 GMT-07:00 Rui Hong notifications@github.com:

Hi Qing,

Thanks for your reply! Could I use dbSNPs information downloaded from UCSC, format them correctly and take this file as SNV list? In this case, the column 5 are all 1. Does this work?

Thanks, Ray

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rz2333 commented 7 years ago

Hi Qing,

Sorry, I misunderstood how does GIREMI work. Now I know how to makes it work. Thanks a lot!

Bests, Ray

On Wed, Oct 5, 2016 at 2:06 PM, zhqingit notifications@github.com wrote:

Hi Ray,

GIREMI is designed to find the RNA editing sites from a mixture of the RNA editing sites and SNPs. I am not clear what's your purpose to input a file with all SNPs?

Best, Qing

2016-10-04 10:03 GMT-07:00 Rui Hong notifications@github.com:

Hi Qing,

Thanks for your reply! Could I use dbSNPs information downloaded from UCSC, format them correctly and take this file as SNV list? In this case, the column 5 are all 1. Does this work?

Thanks, Ray

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/zhqingit/giremi/issues/23#issuecomment-251449188, or mute the thread https://github.com/notifications/unsubscribe-auth/ ALL2zWnte6llmOpGPyC7cIHpyfTPXdp-ks5qwob4gaJpZM4KNBaM

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JohnMCMa commented 7 years ago

I'd need to make a reminder, however--given GATK's HaplotypeCaller and MuTect2 tools performs local reassembly for variant calling, I think it'd be safer to use the tools' bamout as the bam input for GIREMI.