search

FredHutch / Galeano-Nino-Bullman-Intratumoral-Microbiota_2022

Analysis code used in Galeano Nino et al., Impact of Intratumoral Microbiota on Spatial and Cellular Heterogeneity in human cancer. 2022
MIT License
33 stars 10 forks source link

Doubts about the SRA ID #11

Closed februaryfang closed 1 year ago

februaryfang commented 1 year ago

Dear Hanrui, I would like to download the SRA data and test the codes. For each part of the code, I only need data from 2 samples. Can you recommend which SRA to download to me? Currently, I have downloaded Fastq from "https://fh-pi-bullman-s-eco-public.s3.us-west-2.amazonaws.com/DataTransfer/Galeano_Nino_et_al_visium_scans/CRC_OSCC_visium_fastq.tar.gz" for part1.

image image

And I will select the SRA data in the above figure for part 2. Is the SRA ID I have selected correct? Perhaps you can give me a clearer choice.

Best wish, Fang

hanruiw commented 1 year ago

Dear Fang,

Thank you for your interest in our paper. For questions regarding SRA, would you mind send an email to Jorge, who is the first author of this paper. I think he will be able to assist you to choose a suitable sample. Please let me know if you need anything else!

Best regards, Hanrui

februaryfang commented 1 year ago

How can I contact Jorge?

februaryfang commented 1 year ago

And I think there is a lack of data named "1_OSCC_11_GEX_S1_L002_I1_001".

hanruiw commented 1 year ago

jgaleano[a]fredhutch[dot]org