Open rz2333 opened 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
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/zhqingit/giremi/issues/23, or mute the thread https://github.com/notifications/unsubscribe-auth/ALL2zX3284knc1GJ6nZzc8M7OUWXlTHPks5qwWl6gaJpZM4KNBaM .
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 .
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
.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/zhqingit/giremi/issues/23#issuecomment-251752516, or mute the thread https://github.com/notifications/unsubscribe-auth/APrv1goh2AhR1RQRHWGws8iO27glDy1kks5qw-clgaJpZM4KNBaM .
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.
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