search

SJTU-CGM / TGSRICEPAN

The codes of "the Third Generation Sequencing of 111 rice genomes reveals a huge size of novel genome sequence in the RICE PAN-genome"
8 stars 3 forks source link

Questions about 111 genome downloads #2

Open Henry-Ding opened 10 months ago

Henry-Ding commented 10 months ago

hi I found that the download website (https://cgm.sjtu.edu.cn/TGSrice/index.html) given in the article is no longer accessible, is there a new URL published, where else can I go to download? image best wishes henry

chchwei commented 10 months ago

Weird. I can access it from our campus.

Could you try it again in one or two day? I will ask the IT staff member to sort this out.

Best,

Chaochun

发件人: Henry-Ding @.> 发送时间: 2023年11月13日 14:55 收件人: SJTU-CGM/TGSRICEPAN @.> 抄送: Subscribed @.***> 主题: [SJTU-CGM/TGSRICEPAN] Questions about 111 genome downloads (Issue #2)

hi I found that the download website (111 https://cgm.sjtu.edu.cn/TGSrice/index.html ) given in the article is no longer accessible, is there a new URL published, where else can I go to download? https://user-images.githubusercontent.com/56921882/282384413-c8a9694a-6e23-4fd8-ac64-4801e39cde9c.png best wishes henry

— Reply to this email directly, view it on GitHub https://github.com/SJTU-CGM/TGSRICEPAN/issues/2 , or unsubscribe https://github.com/notifications/unsubscribe-auth/ACOKULN63DQPJZ3IIOF2DADYEG73NAVCNFSM6AAAAAA7IVPRU2VHI2DSMVQWIX3LMV43ASLTON2WKOZRHE4DSOJZHAZTCNQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

Henry-Ding commented 10 months ago

hi Thank you for your reply. I tried again and successfully entered the site, probably because of my Internet environment. best wishes henry

Henry-Ding commented 10 months ago

Dear Prof. Wei, I have a new question. I can't find the annotation file (gff3) for each genome on the website, only see the annotation file for the pan-genome, where can I download the annotation file for each genome? best wishes henry

zhixue commented 10 months ago

Dear Prof. Wei, I have a new question. I can't find the annotation file (gff3) for each genome on the website, only see the annotation file for the pan-genome, where can I download the annotation file for each genome? best wishes henry

Hi, we only predicted genes on novel sequences due to limit time, so we provided the gene annotation file for the pan-genome in this paper.

We have already predicted genes on all individual rice genomes in another project. Perhaps it will be released soon, the draft of that project has been submitted.

chchwei commented 10 months ago

Dear Henry,

A new type of genome browser will be available soon from our lab. Could you please wait a few weeks and check the webpage of our lab again?

Thanks,

Chaochun

发件人: Hongzhang Xue @.> 发送时间: 2023年11月17日 15:25 收件人: SJTU-CGM/TGSRICEPAN @.> 抄送: CWei @.>; Comment @.> 主题: Re: [SJTU-CGM/TGSRICEPAN] Questions about 111 genome downloads (Issue #2)

Dear Prof. Wei, I have a new question. I can't find the annotation file (gff3) for each genome on the website, only see the annotation file for the pan-genome, where can I download the annotation file for each genome? best wishes henry

Hi, we only predicted genes on novel sequences due to limit time, so we provided the gene annotation file for the pan-genome in this paper.

We have already predicted genes on all individual rice genomes in another project. Perhaps it will be released soon, the draft of that project has been submitted.

— Reply to this email directly, view it on GitHub https://github.com/SJTU-CGM/TGSRICEPAN/issues/2#issuecomment-1815863061 , or unsubscribe https://github.com/notifications/unsubscribe-auth/ACOKULNS3VGQKFM3PQ6W5RLYE4GNXAVCNFSM6AAAAAA7IVPRU2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJVHA3DGMBWGE . You are receiving this because you commented.Message ID: @.***>