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HongboDoll / TomatoSuperPanGenome

Here, we sequence and de novo assemble chromosome-scale genomes of nine wild species and two cultivated accessions of tomato and constructed a pan-genome, revealing phylogenetic relationships and structural variation among Lycopersicon
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Genomes #3

Open Zhaoqiyue5 opened 4 months ago

Zhaoqiyue5 commented 4 months ago

Hello!

Thank you very much for your contributions and your publicly available data!

I have a question regarding the 11 genomes mentioned in your article. Could you kindly let me know if it is possible to download the FASTQ files for these genomes from any available sources。 So far, I have only found the FASTA and GFF3 files. Additionally, I have not found FASTQ files with the same IDs on NCBI.（https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA809001，https://www.ncbi.nlm.nih.gov/sra）

Thank you,

HongboDoll commented 4 months ago

Hi,

Yes you can find these reads on https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA756391.

HongboDoll commented 4 months ago

Well you can refer to their taxonomic classification

Best Regards,

Hongbo

---- Replied Message ---- | From | @.> | | Date | 08/2/2024 13:25 | | To | @.> | | Cc | @.> , @.> | | Subject | Re: [HongboDoll/TomatoSuperPanGenome] Genomes (Issue #3) |

I saw this, but I can't directly hit their ID between https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA809001 in the ID at https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA756391.

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Zhaoqiyue5 commented 2 months ago

Well you can refer to their taxonomic classification Best Regards, Hongbo … ---- Replied Message ---- | From | @.> | | Date | 08/2/2024 13:25 | | To | @.> | | Cc | @.> , @.> | | Subject | Re: [HongboDoll/TomatoSuperPanGenome] Genomes (Issue #3) | I saw this, but I can't directly hit their ID between https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA809001 in the ID at https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA756391. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

I greatly appreciate your response, which has been of immense help to me. Could you please advise on how I might obtain the GFF3 files of the genomes. Thank you!

HongboDoll commented 2 months ago

https://github.com/HongboDoll/TomatoSuperPanGenome/releases

Best Regards,

Hongbo

---- Replied Message ---- | From | @.> | | Date | 09/18/2024 15:25 | | To | @.> | | Cc | @.> , @.> | | Subject | Re: [HongboDoll/TomatoSuperPanGenome] Genomes (Issue #3) |

Well you can refer to their taxonomic classification Best Regards, Hongbo … ---- Replied Message ---- | From | @.> | | Date | 08/2/2024 13:25 | | To | @.> | | Cc | @.> , @.> | | Subject | Re: [HongboDoll/TomatoSuperPanGenome] Genomes (Issue #3) | I saw this, but I can't directly hit their ID between https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA809001 in the ID at https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA756391. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: @.***>

I greatly appreciate your response, which has been of immense help to me. Could you please advise on how I might obtain the GFF3 files of the genomes. Thank you!

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