search

GoekeLab / sg-nex-data

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
104 stars 24 forks source link

fast5 file unable to download now #6

Closed MengZou1 closed 2 years ago

MengZou1 commented 3 years ago

Hi I am doing some analysis on RNA modifications and I need to download the raw fast5 file for dRNA-seq data. But the link is not available now. Another question, when your lab will relase other cell line?

jonathangoeke commented 3 years ago

Hi @MengZou1 the fast5 files are too large to be hosted with the current file hosting service, but we look into how to make them available, hopefully in the next weeks (likely through ENA). You can sign up to the email list where we will post any update: https://groups.google.com/forum/#!forum/sg-nex-updates/join

MengZou1 commented 3 years ago

@jonathangoeke Thank you very much. I have joined the group. Hopefully see these raw files in the next weeks.

MengZou1 commented 3 years ago

Hi @jonathangoeke ,I am wondering I am not recieving the latest news about the raw fast5 data although I have joined the email list. Hoping to see the good news. Thank you.

jonathangoeke commented 3 years ago

Hi @MengZou1 yes we still did not finish the upload of the fast5 files, I will post an update here and on the email list then. In the meantime you could use these data here for a start: https://www.ebi.ac.uk/ena/browser/view/PRJEB40872 (from this study: https://www.biorxiv.org/content/10.1101/2020.06.18.160010v1)

MengZou1 commented 3 years ago

Hi @jonathangoeke , Thank you very much. I will have a careful look.

MengZou1 commented 3 years ago

Hi @jonathangoeke, Could you tell more information about the data? It is a little difficult to know which one is raw fast5 for WT form the sample name.

jonathangoeke commented 3 years ago

Hi @MengZou1 you can find out from the file names (eg ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR470/ERR4706156/HEK293T-WT-rep1.tar.gz is fast5 for WT; ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR470/ERR4706158/HEK293T-Mettl3-KO-rep1.fastq.gz is fastq for KO). The file format is also described in the additional columns

MengZou1 commented 3 years ago

Hi @jonathangoeke , Thank you very much and I have found rep1 and rep3 for WT and KO but no rep2? I am also a little confused about other samples, for example, HEK293T-WT-25-rep4.tar.gz, it has rep4? what is the meaning of "25" ?

MengZou1 commented 3 years ago

I am wobdering is there something in my download data? Usually it would be stoped for unkown reason. Besides, I could not find the HEK293T-WT-rep2.tar.gz in the list.

lwlive commented 3 years ago

I also need the raw fast5 files, but I can only find fastq files in EBI(https://www.ebi.ac.uk/ena/browser/view/PRJEB40872) and xpore(https://zenodo.org/record/5103099#.YPlv2tOf6UF). It seems fast5 files are necessary when performing Data preparation from raw reads in commands "nanopolish index -d <PATH/TO/FAST5_DIR> <PATH/TO/FASTQ_FILE>". Could you offer me the direct link to donwload the fast5 files? Thank you!

ronicaa commented 3 years ago

I'm waiting for the fast5 files as well.

jonathangoeke commented 3 years ago

Hi @lwlive @MengZou1 @ronicaa the files from these links are the Hek293T cell line, the fast5 should be available. If the download links are not working, can you post this here instead?

The fast5 files are required for data preprocessing, for analysis with xPore the files from the zenodo link will work.

Thanks!

ronicaa commented 3 years ago

@jonathangoeke Thank you very much! I've found those fast5 files!