search

BGI-shenzhen / LDBlockShow

LDBlockShow: a fast and convenient tool for visualizing linkage disequilibrium and haplotype blocks based on VCF files
MIT License
134 stars 40 forks source link

non-human genome #28

Closed chengroup closed 8 months ago

chengroup commented 1 year ago

Hello,

When use LDBlockShow to non-human genome, how to set the chromosome set?

Thanks in avance!

C

hewm2008 commented 1 year ago

Hi: LDblockshow is mainly to view the ld block(LDheatmap) of a specific region, and the region is determined by the -Region parameter [ -Region chr:start:end ] The program recommends that the number of snp should not exceed 1w, and it is best to control it at 5k sites. Here I provide a script that randomly selects an snp every XXX bps issues4

zzzzzd0825 commented 1 year ago

Hi: Did you solve with it？

chengroup commented 1 year ago

Yes, I successfully did it. Thanks!

On Wed, Jun 14, 2023 at 3:24 PM zzzzzd0825 @.***> wrote:

Hi: Did you solve with it？

— Reply to this email directly, view it on GitHub https://github.com/BGI-shenzhen/LDBlockShow/issues/28#issuecomment-1590623833, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACSK4GDBRQ2IEPKIO2Q7D43XLFRKHANCNFSM6AAAAAAREZGRWI . You are receiving this because you authored the thread.Message ID: @.***>

-- Ph.D., Associate Professor College of Animal Science and Technology Sichuan Agricultural University Chengdu, Sichuan, 611130 China Email: @., @. Google Scholar: https://scholar.google.com/citations?user=CEXO6hMAAAAJ&hl=en ResearchGate: https://researchgate.net/profile/Shi-Yi-Chen

zzzzzd0825 commented 1 year ago

HI： I'm sorry, I also met the same problem, how did you solve it？

zzzzzd0825 commented 1 year ago

I can't find any option to fix it

chengroup commented 1 year ago

I used the " -Region 14:308359:438267" to view the specific genomic region.

On Wed, Jun 14, 2023 at 5:06 PM zzzzzd0825 @.***> wrote:

I can't find any option to fix it

— Reply to this email directly, view it on GitHub https://github.com/BGI-shenzhen/LDBlockShow/issues/28#issuecomment-1590798412, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACSK4GBK6ITTFAZKSYQJMMTXLF5IZANCNFSM6AAAAAAREZGRWI . You are receiving this because you authored the thread.Message ID: @.***>

-- Ph.D., Associate Professor College of Animal Science and Technology Sichuan Agricultural University Chengdu, Sichuan, 611130 China Email: @., @. Google Scholar: https://scholar.google.com/citations?user=CEXO6hMAAAAJ&hl=en ResearchGate: https://researchgate.net/profile/Shi-Yi-Chen

zzzzzd0825 commented 1 year ago

I will try it. Thanks！ ---- Replied Message ---- | From | @.> | | Date | 06/14/2023 19:58 | | To | BGI-shenzhen/LDBlockShow @.> | | Cc | zzzzzd0825 @.>, Comment @.> | | Subject | Re: [BGI-shenzhen/LDBlockShow] non-human genome (Issue #28) |

I used the " -Region 14:308359:438267" to view the specific genomic region.

On Wed, Jun 14, 2023 at 5:06 PM zzzzzd0825 @.***> wrote:

I can't find any option to fix it

— Reply to this email directly, view it on GitHub https://github.com/BGI-shenzhen/LDBlockShow/issues/28#issuecomment-1590798412, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACSK4GBK6ITTFAZKSYQJMMTXLF5IZANCNFSM6AAAAAAREZGRWI . You are receiving this because you authored the thread.Message ID: @.***>

-- Ph.D., Associate Professor College of Animal Science and Technology Sichuan Agricultural University Chengdu, Sichuan, 611130 China Email: @., @. Google Scholar: https://scholar.google.com/citations?user=CEXO6hMAAAAJ&hl=en ResearchGate: https://researchgate.net/profile/Shi-Yi-Chen

— Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>