Submit read data to ENA

For a step-by-step instruction see https://fgcz-gstore.uzh.ch/public/guides/ENA-submission.pdf.

Register here: https://www.ebi.ac.uk/ena

Upload reads

Create for each fastq.gz file an md5 file. You can do this from the existing md5.txt file in your reads folder

ssh YOUR_BFABRIC_USERNAME@fgcz-genomics.uzh.ch
awk -F '\t' '{print $1 > $2".md5"}' /srv/gstore4users/pXXXXX/HiseqXXXXXXX/md5.txt

Alternatively you can also compute it. Note this may take a while.
Create for each fastq.gz file also an md5 file. Upload both

md5sum  /srv/gstore4users/pXXXXX/HiseqXXXXXXX/file.name.fastq.gz  | cut  -d “ “ –f1 >  file.name.fastq.gz.md5

Upload the md5 files

ssh YOUR_BFABRIC_USERNAME@fgcz-genomics.uzh.ch
ftp webin.ebi.ac.uk
#set the following: 
bin 
passive 
prompt
#to upload gezipped files run:
mput *md5
## after everything is done type
bye

Upload the read files

ssh YOUR_BFABRIC_USERNAME@fgcz-genomics.uzh.ch
## start a screen with
screen -S webin
cd /srv/gstore4users/pXXX
cd HiSeqXXXX
ftp webin.ebi.ac.uk
#set the following: 
bin 
passive 
prompt
#to upload gezipped files run:
mput *gz
## after everything is done type
bye
## now stop the screen
Ctrl-D
## log off the fgcz-genomics

For genome informatics team:
Webin submission account: Webin-67057
Password: GenomeInformatics2024!

Upload the md5 files

lftp webin2.ebi.ac.uk -u Webin-xxxxx
#to upload gezipped files run:
mput *md5
## after everything is done type
bye

Upload the read files

## start a screen with
screen -S webin
lftp webin2.ebi.ac.uk -u Webin-xxxxx
#to upload gezipped files run:
mput *gz
## after everything is done type
bye
## now stop the screen
Ctrl-D
## log off